Compositions and methods comprising sequences having hydroxyphenylpyruvate dioxygenase (HPPD) activity

ABSTRACT

Compositions and methods comprising polynucleotides and polypeptides having 4-hydroxyphenylpyruvate dioxygenase (HPPD) activity and having insensitivity to an HPPD inhibitor are provided. Further provided are nucleic acid constructs, plants, plant cells, explants, seeds and grain having the HPPD sequences. Various methods of employing the HPPD sequences are provided. Such methods include, for example, methods for producing an HPPD inhibitor tolerant plant, plant cell, explant or seed and methods of controlling weeds in a field containing a crop employing the plants and/or seeds disclosed herein. Methods are also provided to identify additional HPPD variants. Further provided are various methods and compositions that allow the various HPPD polypeptides and variant and fragments thereof to be expressed in a chloroplast or transported to a chloroplast.

CROSS-REFERENCE TO RELATED APPLICATIONS

This Application claims the benefit of U.S. Provisional Application No.61/987,965, filed on May 2, 2014, which is incorporated herein byreference in its entirety.

REFERENCE TO A SEQUENCE LISTING SUBMITTED AS A TEXT FILE VIA EFS-WEB

The official copy of the sequence listing is submitted electronicallyvia EFS-Web as an ASCII formatted sequence listing with a file named36446_0199P1_Sequence_Listing.txt, created on May 2, 2015, and having asize of 356,801 bytes and is filed concurrently with the specification.The sequence listing contained in this ASCII formatted document is partof the specification and is herein incorporated by reference in itsentirety.

BACKGROUND OF THE INVENTION

In the commercial production of crops, it is desirable to easily andquickly eliminate unwanted plants (i.e., “weeds”) from a field of cropplants. An ideal treatment would be one which could be applied to anentire field but which would eliminate only the unwanted plants whileleaving the crop plants unharmed. One such treatment system wouldinvolve the use of crop plants which are tolerant to a herbicide so thatwhen the herbicide was sprayed on a field of herbicide-tolerant cropplants, the crop plants would continue to thrive whilenon-herbicide-tolerant weeds were killed or severely damaged. Ideally,such treatment systems would take advantage of varying herbicideproperties so that weed control could provide the best possiblecombination of flexibility and economy. For example, individualherbicides have different longevities in the field, and some herbicidespersist and are effective for a relatively long time after they areapplied to a field while other herbicides are quickly broken down intoother and/or non-active compounds. An ideal treatment system would allowthe use of different herbicides so that growers could tailor the choiceof herbicides for a particular situation.

Crop tolerance to specific herbicides can be conferred by engineeringgenes into crops which encode appropriate herbicide metabolizing enzymesand/or insensitive herbicide targets. In some cases these enzymes, andthe nucleic acids that encode them, originate in a plant. In othercases, they are derived from other organisms, such as microbes. See,e.g., Padgette et al. (1996) “New weed control opportunities:Development of soybeans with a Roundup Ready® gene” and Vasil (1996)“Phosphinothricin-resistant crops,” both in Herbicide-Resistant Crops,ed. Duke (CRC Press, Boca Raton, Fla.) pp. 54-84 and pp. 85-91. Indeed,transgenic plants have been engineered to express a variety of herbicidetolerance genes from a variety of organisms.

For nearly two decades, corn, soybean, and cotton farmers have relied onglyphosate and glyphosate resistant crops for weed control. Whilefavored for its efficacy, economy and convenience, the onset ofglyphosate-resistant weeds, now numbering 26 species (Heap, 2014),signals a need for new herbicide and trait systems that meet similarcriteria (Green and Castle, 2010; Duke, 2012). The silver bulletsolution would be another herbicide and trait combination as effectiveas glyphosate. Unfortunately, prospects for novel herbicide chemistriesare not encouraging (Duke, 2012).

Inhibitors of 4-hydroxyphenylpyruvate dioxygenase (HPPD) disruptproduction of tocopherols (antioxidants) and plastoquinone (essentialfor photosynthetic electron transfer) by blocking conversion oftyrosine, through 4-hydroxyphenyl pyruvate (HPP), to homogentisate(Moran, 2014). The result is that the plant cannot protect itself fromthe radicals generated by light activation of chlorophyll, causingbleaching, necrosis, and death. Registered HPPD inhibitors includemesotrione, tembotrione, sulcotrione, isoxaflutole, and topramezone.HPPD inhibitors are most effective on broad-leaf weeds but control somegrasses as well. Currently, HPPD herbicides are selective for use incorn, while soybeans and other dicot crop species are sensitive. A broadspectrum HPPD tolerance trait in soybeans, used in combination withglyphosate tolerance and other traits or selective herbicides, willprolong the positive impact of the glyphosate systems and slowappearance of resistant weeds. Two such products, one for tolerance toisoxaflutole (APHIS, 2009) and the other to mesotrione and isoxaflutole(APHIS, 2012) are in the USDA regulatory approval process. The formeruses a Pseudomonas fluorescens HPPD with a single amino acid change(Matringe et al., 2005), while the latter uses HPPD from oat, with asingle amino acid change (Hawkes et al., 2010). There are presently noreports of tembotrione or broad spectrum tolerance.

To develop a robust and stable HPPD tolerance trait in soybean,expression patterns of the native gene and localization of native andtransgenic protein were studied, and the efficacy of low to moderateexpression of a desensitized protein were evaluated. Data regarding thesubcellular location of HPPD are ambiguous, perhaps resulting fromspecies diversity. Early work with organelle fractions attributed mostHPPD activity to the chloroplast in spinach (Fiedler et al., 1982) orLemna gibba (Loeffelhardt and Kindl, 1979). Organelle targeting can beconjectured from the observation that the N-terminal sequence of matureHPPD isolated from maize leaf begins at either ala-17 (Fritze et al.,2004) or ala-23 (Yang et al., 2004) with respect to the translatedfull-length gene. Two HPPD genes identified from EST libraries preparedfrom cotton tissue were 98.6 percent identical, each with a 23-aminoacid sequence deemed likely to function in chloroplast targeting byanalysis with the ChloroP prediction program (Moshiri et al., 2007). Inthe same publication, tomato, but not Brassica HPPD was predicted tohave a CTP. Subcellular fractionation supported a cytosolic location ofthe carrot cell enzyme (Garcia et al., 1997). Although the N-terminalsequence of the purified enzyme was truncated with respect to thetranslated cDNA, this was attributed to proteolysis during purification.Later, the same authors determined that after PSORT analysis failed toidentify a targeting signal within the Arabidopsis HPPD amino acidsequence, native Arabidopsis HPPD heterologously expressed in tobaccowas located exclusively in the cytosol (Garcia et al., 1999).

While a number of HPPD crop plants are presently commercially available,improvements in every aspect of crop production, weed control options,extension of residual weed control, and improvement in crop yield arecontinuously in demand. Particularly, due to local and regionalvariation in dominant weed species as well as preferred crop species, acontinuing need exists for customized systems of crop protection andweed management which can be adapted to the needs of a particularregion, geography, and/or locality. A continuing need therefore existsfor compositions and methods of crop protection and weed management.

BRIEF SUMMARY OF THE INVENTION

Compositions and methods comprising polynucleotides and polypeptideshaving 4-hydroxyphenylpyruvate dioxygenase (HPPD) activity and having aninsensitivity to at least one HPPD inhibitor are provided. Furtherprovided are nucleic acid constructs, plants, plant cells, explants,seeds and grain having the HPPD sequences.

Various methods of employing the HPPD sequences are provided. Suchmethods include methods for producing an HPPD inhibitor tolerant plant,plant cell, explant or seed and methods of controlling weeds in a fieldcontaining a crop employing the plants and/or seeds disclosed herein.

Methods are also provided to identify additional HPPD variants.

Further provided are methods and compositions that allow the variousHPPD polypeptides and variants and fragments thereof to be expressed ina chloroplast or transported to a chloroplast. Such methods andcompositions find use in producing plant cells, plants and explantshaving tolerance to various HPPD inhibitors.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1. Structures of herbicidal HPPD inhibitors and a HPPD substrate,4-hydroxyphenylpyruvate.

FIG. 2. HPPD inhibitor herbicide site of action and symptoms. FIG. 2A:HPPD reaction and essential downstream products in plants. FIG. 2B:Bleaching symptoms of HPPD-inhibiting herbicides in soybean.

FIGS. 3A-3M. Z. mays HPPD protein characterization. FIG. 3A: Z. maysHPPD amino acid sequence. FIG. 3C: Fluorescence observed in chloroplastsof maize leaf expressing rubisco activase CTP-Ds-Red2, with the samesample photographed under white light shown in FIG. 3B. FIG. 3E:Fluorescence observed in chloroplasts of maize leaf expressingN-terminal 50 amino acids of maize HPPD-Ds-Red2, with the same samplephotographed under white light shown in FIG. 3D. FIG. 3G: Fluorescenceobserved in cytosol of maize leaf expressing untargeted Ds-Red2, withthe same sample photographed under white light shown in FIG. 3F. FIGS.3H-3J: Maize cells transiently expressing DsRed fused to 30, 40 and 50amino acid N-terminal region of HPPD protein sequence (FIGS. 3H, 3I, and3J, respectively). FIG. 3K: Expression in both chloroplasts andcytoplasm of soybean leaf epidermal cell transiently expressing AcGFPfused to amino acids 1-50 of maize HPPD. FIG. 3L: Expression inchloroplasts of guard cells in soybean stably expressing AcGFP linked toamino acids 1-50 of maize HPPD. FIG. 3M: alignment of monocot HPPDN-terminal region sequences (Avena sativa HPPD WO0246387 (SEQ ID NO:102), Hordeum vulgare HPPD 048604.1 (SEQ ID NO: 103), Triticum aestivumHPPD AAZ67144.1 (SEQ ID NO: 104), Oryza sativa HPPD BAD26248.1 (SEQ IDNO: 105), Sorghum bicolor HPPD XP_002453359 (SEQ ID NO: 106), and Zeamays_WO1997049816Seq#11 (SEQ ID NO: 107)) and consensus monocotfunctional CTP (SEQ ID NO: 94). Sources of sequences are indicated. Grayshading shows identities in sequences.

FIGS. 4A-4F. Genomic analysis of soybean HPPD. FIG. 4A: G. max HPPDprotein sequence (SEQ ID NO: 100) with in-frame N-terminal extension(underlined). FIG. 4B: Protein gel of in vitro transcription-translationproducts of the two (3′ truncated) HPPD transcripts. Predicted proteinmass from −237 mRNA: 30.6 kD; +1 mRNA: 26.0 kD. FIG. 4C: Transientexpression of N-terminal fragment 1-44 with DsRed2 in soybean. FIG. 4D:Transient expression of N-terminal fragment 42-86 with AcGFP1 insoybean. FIG. 4E: Transient expression of N-terminal fragment 1-86 withAcGFP1 in soybean. FIG. 4F, Alignment of Z. mays (SEQ ID NO: 1) and G.max (SEQ ID NO: 100) HPPD proteins. An asterisk indicates identity; acolon shows the fusion point of soybean to maize insensitive HPPDproteins.

FIG. 5. Progression of enzyme fitness with rounds of shuffling. Barsindicate ON and OFF rate ratios, the insensitivity parameters that arefunctions of the rate constants for association and dissociation ofenzyme and inhibitor, respectively. “Fitness” is the product ofk_(cat)/K_(m) and insensitivity parameters (ON rate ratio and OFF rateratio, see text for details), and approximates k_(cat)/K_(m)×K_(i).

FIG. 6. Selection for insensitivity to mesotrione or tembotrioneresulted in cross-insensitivity to other herbicidal inhibitors.“Fitness” is the product of k_(cat)/K_(m) and insensitivity parameters,and approximates k_(cat)/K_(m)×K_(i). The dotted line is drawn at thefitness level that provided tolerance in soybean to twice the labeledfield rate (for maize) of tembotrione in 2013 field trials.

FIG. 7. Expression of soybean HPPD ESTs in specific tissues compared toEPSPS and ALS with ACT2/7 as a moderately expressing control gene. Unitsof expression are reads/kilobase/million, normalized from raw data(SoyBase.org).

FIGS. 8A and 8B. FIG. 8A: Upstream 1225 bp G. max promoter sequence andN-terminal regions of the long and short HPPD proteins (nucleotidesequence set forth as SEQ ID NO: 108; amino acid sequence shown in FIG.8A corresponds to the first fifty-seven amino acids of SEQ ID NO: 100).Underlined bold denotes predicted TATA sequences; bold denotesmethionine initiation sites for long and short proteins; grey backgrounddenotes actual transcription start sites at positions −237 and +1.; Greybox denotes the upORF in the long transcript. FIG. 8B: Schematic of G.max HPPD promoter and coding region.

FIGS. 9A-9D. Field trial with transgenic soybean events treated with 2×maize field rate of tembotrione, 14 days after treatment. FIG. 9A:Promoter HSP206 and full length maize HPPD variant 6-1. FIG. 9B: 35Senhanced promoter SHP110 with fused Gm:Zm HPPD variant 6-1. FIG. 9C:Non-transgenic unsprayed control. FIG. 9D: Non-transgenic sprayedcontrol. Treatment was as described in Table 6.

FIGS. 10A and 10B. FIG. 10A: Immuno-localization of native HPPD in maizeleaf shows label only in chloroplasts. Serum containing anti-maize oranti-soybean HPPD antibodies was raised in rabbits inoculated withrecombinant wild-type 6×-his-HPPD produced in E. coli and purified bynickel chelate affinity chromatography. The serum was passed throughProtein A Ceramin Hyper DF to adsorb the IgG fraction. After washing,IgG was eluted with citrate buffer, pH 2.55, with a yield of 50 mg ofIgG per gram of serum protein. Ten mg of IgG protein were subjected tothe manufacturer's linkage protocol for Affi-Gel Hz (Bio-Rad, Hercules,Calif.), which, in the case of the maize enzyme, resulted in the captureof 2 mg of IgG, 20% of which was anti-maize HPPD. Anti-HPPD antibodieswere further purified by passage through a column of immobilizedRubisco, to remove a small fraction of antibodies that reacted with bothHPPD and Rubisco. Leaf punches from mature line A63 maize plants ornative or stably transformed soybean plants expressing a gene encodingthe maize HPPD protein driven by an SCP1 synthetic promoter (Cahoon andCoughlan, 2007) were fixed in 2% paraformaldehyde, 0.25% glutaraldehydein 100 mM Na phosphate buffer, pH 7.0, for 3 hours at room temperature,dehydrated by passage through progressively higher concentrations ofethanol, embedded in LR White resin and cured at 55° C. for 48 hours.Immuno-localizations were performed with the primary antibody being thedouble-purified anti-maize HPPD (1:200) and the secondary antibody goatanti-rabbit F(ab′) conjugated with μltrasmall gold particles (Aurion,The Netherlands). Gold labeling was followed by silver enhancement(Aurion). Sections were counterstained with 4% uranyl acetate (aqueous)followed by Reynold's lead citrate and examined with a Hitachi S4800scanning electron microscope. Gold labeling was observed mainly inbundle sheath chloroplasts (range; 5-28 particles per chloroplast, 50chloroplasts observed. The highest frequency of observations was 6chloroplasts that contained 8 particles. Particles were also found inmesophyll chloroplasts, 31 of which had 1 to 5 particles and 19, ofwhich had no particles. A small number of particles were also observedrandomly in other locations including cytosol and voids, and wereconsidered to be artifacts. FIG. 10B: shows the inner indicatedrectangle at higher digital magnification.

FIGS. 11A-11J. The N-terminal 50 amino acids of maize HPPD directsfluorescent protein to the chloroplasts of maize leaf guard cells. FIGS.11A-11D, Co-expression of untargeted C3GFP and HPPD N-terminal50AA::DsRed2. FIGS. 11E-11G, Co-expression of untargeted C3GFP andRubisco activase CTP::DsRed. FIGS. 11H-11J, untargeted C3GFP. The redchannel (FIGS. 11B, 11F and 11I) shows the pattern of DsRedfluorescence, the green channel (FIGS. 11D, 11G, and 11J) showsuntargeted C3GFP fluorescence and the blue channel (FIG. 11C),chlorophyll autofluorescence. Overlays of the red and green channels areshown in FIGS. 11A, 11E and 11H. Plastid targeting by the N-terminal 50amino acids of maize HPPD is evident from the co-localization of theDsRed with chlorophyll autofluorescence (FIGS. 11B and 11C) and the lackof overlap with the untargeted C3CFP (FIGS. 11B and 11D). Note thatexclusion of the C3GFP signal marks the location of the guard cellplastids. Similarly, the positive control vector for chloroplastlocalization showed a lack of overlap between the cytosolic C3GFP signaland the DsRed signal (FIGS. F and G). Untargeted DsRed shows spatialoverlap of the DsRed and C3GFP signals and an absence of DsRed in theregions of C3GFP exclusion that mark the position of the plastids. Maizeseedlings were generated in the absence of soil by embedding kernelsbetween two sheets of blotting paper hydrated in tap water amended with0.1 mg/ml sucrose. Leaf segments were detached from seedlings at 15 dayspost-planting immediately before biolistic transformation. The lowerepidermis of the leaf segments was bombarded and the segments wereplaced in sterile moist chambers. The tissue was co-bombarded with DNAfrom DsRed-containing test plasmids and a plasmid encoding untargetedCycle 3 Green Fluorescence Protein (C3GFP, Life Technologies) using thePDS-1000 He biolistic particle delivery system (Bio-Rad, HerculesCalif.). Gold particles (0.6 m in diameter; Bio-Rad) were coated withplasmid DNA as follows. Fifty μl of freshly prepared gold particles inwater (20 mg/ml), and 20 μl of DNA mixture (containing 10 μg ofequimolar quantities of the DsRed-containing test plasmid and theuntargeted C3GFP plasmid) were combined. While gently vortexing, 50 μlof a 2.5 M CaCl2 solution and 20 μl of freshly prepared 0.1 M spermidine(Sigma-Aldrich, St Louis Mo.) were slowly added. The mixture wasincubated at room temperature for 5 min and pelleted at 13,000 g in amicro-centrifuge for 5 sec. The supernatant was carefully removed andthe pellet was resuspended in 85 μl of 100% ethanol. While gentlyvortexing, a 5 μl aliquot of suspension was drawn and dispensed onto thecenter of a macrocarrier membrane. The membrane was allowed to drycompletely for 2-5 min and used immediately. Leaf segments werebombarded at a distance of 9 cm from an 1100-psi rupture disk. Threereplicate shots were performed from each coating preparation. Initialexamination was conducted at approximately 24 h post-bombardment with aLumar fluorescence stereomicroscope (Carl Zeiss Inc., Thornwood N.Y.)equipped with both a UV-exciting (Zeiss Set 01) and red-emitting (ZeissSet 43 HE) filter set to image the C3GFP and the DsRed2, respectively.The leaf segments containing DsRed2-positive cells identified in thestereomicroscope were placed in a 0.01% Tween 20 solution and a vacuumwas applied for about 10 min to remove internal air and to wet the leafsurface. The leaves were placed into coverglass chambers in the samesolution, sealed with an additional coverglass and examined in theLSM510 (Carl Zeiss). C3GFP fluorescence was captured using a 488 nmargon laser for excitation and a 500-550 nm band pass emission filter.DsRed fluorescence was imaged using a 561 nm diode laser for excitationand a 575-615 nm band pass emission filter. Chlorophyll fluorescence wascaptured by combining 561 nm excitation and a 650-710 nm band passemission filter.

FIGS. 12A and 12B. Each of FIGS. 12A and 12B show immuno-localizationelectron microscopy of HPPD in soybean cotyledons shows label inchloroplasts and cytoplasm. Affinity purified rabbit anti-soy HPPDantibody was obtained as described for FIGS. 10A and 10B. Pieces ofgreen soybean cotyledon (6 days after planting) were cut under fixative(4% paraformaldehyde, 0.1% glutaraldehyde, 0.1 M sucrose in 0.1M NaPhosphate Buffer, pH 7.2) and held in fixative for 20 min under vacuumat room temperature, then overnight at 4° C. Sectioning, labeling,counterstaining and microscopy were as in FIG. 1S with 10 nm gold. Goldparticles were observed exclusively in chloroplasts and cytosol. Most ofthe fields captured show a greater portion of the label in chloroplasts.

FIGS. 13A-13D. Indirect measurement of rates of association anddissociation of inhibitors and HPPD. Rates of association (k_(ON)) arerepresented by inactivation during catalytic turnover. At time 0,reactions are started with the simultaneous addition of HPP andinhibitor to an aliquot of enzyme. Reaction rates in the 70 to 90 secinterval are recorded and expressed as the ratio of the rate withinhibitor to that with no inhibitor. FIGS. 13A and 13B: Time course,reaction with wt maize HPPD or a shuffled variant; 100 μM HPP±4 μMmesotrione. For wild type maize HPPD, rapidly slowing reaction indicatesa relatively high k_(ON). For the shuffled variant, resistance toinactivation indicates a lower value for k_(ON). The smaller the actualk_(ON), the more slowly the HPPD reaction decelerates and the higher thevalue is for the ON rate ratio. FIGS. 13C and 13D: OFF rate ratio. Aquantitative indicator of k_(OFF) was obtained by observing the timecourse of an HPPD reaction as inhibitor is released from a pre-formedenzyme-inhibitor complex. The ratio of the maximum rate attained inmixtures containing inhibitor to the initial velocity of mixtureslacking inhibitor is termed the “OFF rate ratio”. The plateau ofabsorbance is due to exhaustion of the substrate. With improvedvariants, not only was the steady state attained in a shorter time span,the velocity attained was higher than with wild type, though the enzymeswere present at the same concentration (240 nM). This is because alarger fraction of the variant enzyme was free of inhibitor compared tothe wild-type enzyme, which can due to a higher KD.

FIG. 14. The figure shows data indicating the influence of transgeneexpression level on trait efficacy and plant phenotype of soybean plantstreated with tembotrione in the field. Tembotrione was applied at 180g/ha (twice the labeled rate for maize) at the V4 stage. Phenotype wasrated on mature plants in late summer. Filled diamonds: Injury rating,0, no injury, 100, dead plant; 14 days after treatment. Open circles:Phenotype rating; 20, no symptoms; 1, leaf crinkling, empty seed pods.Correlation (R2), log plot, for injury versus protein=0.48. Correlation(R2), linear regression, for phenotype versus protein=0.70.

FIG. 15. Kinetic parameters, insensitivity parameters, trait fitnessparameters, and trait fitness (fold vs. wild-type) for the indicatedmutants is given. The various data were determined using the methodsdescribed herein below. In the figure, the following abbreviations areused: “Tembo” indicates tembotrione; “Meso” indicates mesotrione;“Sulco” indicates sulcotrione; “Isox(DKN)” indicates isoxaflutole(diketonitrile); and “Topra” indicates topramezone.

FIG. 16. The figure shows the chemical structures for various HPPDinhibitors.

FIG. 17. The figure shows the enzymatic conversion of4-hydroxyphenylpyruvate by HPPD to homogentisate, and the subsequentenzymatic conversion of homogentisate to maleylacetoacetate by HGD. Thedetection parameters for maleylacetoacetate are shown in the figure.

DETAILED DESCRIPTION OF THE INVENTION

The present disclosure now will be described more fully hereinafter withreference to the accompanying drawings, in which some, but not allembodiments or aspects are shown. Indeed, the disclosure may be embodiedin many different forms and should not be construed as limited to theembodiments set forth herein; rather, these embodiments are provided sothat this disclosure will satisfy applicable legal requirements. Likenumbers refer to like elements throughout.

Many modifications and other embodiments of the disclosure set forthherein will come to mind to one skilled in the art to which thisdisclosure pertains having the benefit of the teachings presented in theforegoing descriptions and the associated drawings. Therefore, it is tobe understood that the disclosure is not to be limited to the specificembodiments disclosed and that modifications and other embodiments areintended to be included within the scope of the appended claims.Although specific terms are employed herein, they are used in a genericand descriptive sense only and not for purposes of limitation.

I. Compositions

A. Hydroxyphenylpyruvate Dioxygenase (HPPD) Polynucleotides andPolypeptides

Hydroxyphenylpyruvate dioxygenase (HPPD) converts hydroxyphenylpyruvate,derived from the aromatic amino acid biosynthesis pathway, tohomogentisate. Homogentisate is a precursor of tocopherols andplastoquinones, an electron carrier essential in the biosynthesis ofcarotenoids. Consequently, when HPPD is inhibited by herbicideinhibitors, the plant can not protect itself from the radicals generatedby light activation of chlorophyll. More specifically, inhibition ofHPPD polypeptide leads to the depletion of protective pigments in theplant tissue resulting in bleaching of tissues which leaves the plantsvulnerable to damage by light. HPPD inhibitors are an important class ofherbicides, and transgenes that confer crop tolerance to HPPD inhibitorswould be of significant value, especially for managing weed resistanceto glyphosate.

As used herein, “hydroxyphenylpyruvate dioxygenase,” “HPPD,” “4-hydroxyphenyl pyruvate (or pyruvic acid) dioxygenase (4-HPPD),” and “p-hydroxyphenyl pyruvate (or pyruvic acid) dioxygenase (p-OHPP)” are synonymousand refer to a non-heme iron-dependent oxygenase that catalyzes theconversion of 4-hydroxyphenylpyruvate to homogentisate (see FIG. 17). Inorganisms that degrade tyrosine, the reaction catalyzed by HPPD is thesecond step in the pathway. In plants, formation of homogentisate isnecessary for the synthesis of plastoquinone, an essential redoxcofactor, and tocopherol (see FIG. 2A). The structures of various HPPDpolypeptides are known.

Various methods and compositions are provided which employ polypeptideshaving HPPD activity and having an increased insensitivity to at leastone HPPD inhibitor when compared to an appropriate control, and thepolynucleotides encoding these polypeptides. In an aspect, HPPDpolypeptides having HPPD activity and having an increased insensitivityto at least one HPPD inhibitor when compared to an appropriate controlinclude those set forth in any one of SEQ ID NO:2-83, and biologicallyactive variants and fragments thereof. In various aspects, HPPDpolypeptides having HPPD activity and having an increased insensitivityto at least one HPPD inhibitor when compared to an appropriate controlinclude those set forth in any one of SEQ ID NO:4, 7, 8, 18, and 22, andbiologically active variants and fragments thereof. Further provided arethe polynucleotides encoding these various polypeptides and activevariants and fragments thereof.

As used herein, an “isolated” or “purified” polynucleotide orpolypeptide, or biologically active portion thereof, is substantially oressentially free from components that normally accompany or interactwith the polynucleotide or polypeptide as found in its naturallyoccurring environment. Thus, an isolated or purified polynucleotide orpolypeptide is substantially free of other cellular material or culturemedium when produced by recombinant techniques, or substantially free ofchemical precursors or other chemicals when chemically synthesized. Invarious aspects, an “isolated” polynucleotide is free of sequences(optimally protein encoding sequences) that naturally flank thepolynucleotide (i.e., sequences located at the 5′ and 3′ ends of thepolynucleotide) in the genomic DNA of the organism from which thepolynucleotide is derived. For example, in various embodiments, theisolated polynucleotide can contain less than about 5 kb, 4 kb, 3 kb, 2kb, 1 kb, 0.5 kb, or 0.1 kb of nucleotide sequence that naturally flankthe polynucleotide in genomic DNA of the cell from which thepolynucleotide is derived. A polypeptide that is substantially free ofcellular material includes preparations of polypeptides having less thanabout 30%, 20%, 10%, 5%, or 1% (by dry weight) of contaminating protein.In an aspect, a disclosed polypeptide, or biologically active portionthereof, is recombinantly produced, culture medium represents less thanabout 30%, 20%, 10%, 5%, or 1% (by dry weight) of chemical precursors ornon-protein-of-interest chemicals.

As used herein, polynucleotide or polypeptide is “recombinant” when itis artificial or engineered, or derived from an artificial or engineeredprotein or nucleic acid. For example, a polynucleotide that is insertedinto a vector or any other heterologous location, e.g., in a genome of arecombinant organism, such that it is not associated with nucleotidesequences that normally flank the polynucleotide as it is found innature is a recombinant polynucleotide. A polypeptide expressed in vitroor in vivo from a recombinant polynucleotide is an example of arecombinant polypeptide. Likewise, a polynucleotide sequence that doesnot appear in nature, for example, a variant of a naturally occurringgene is recombinant.

A “control” or “control plant” or “control plant cell” provides areference point for measuring changes in phenotype of the subject plantor plant cell, and may be any suitable plant or plant cell. A controlplant or plant cell may comprise, for example: (a) a wild-type or nativeplant or cell, i.e., of the same genotype as the starting material forthe genetic alteration which resulted in the subject plant or cell; (b)a plant or plant cell of the same genotype as the starting material butwhich has been transformed with a null construct (i.e., with a constructwhich has no known effect on the trait of interest, such as a constructcomprising a marker gene); (c) a plant or plant cell which is anon-transformed segregant among progeny of a subject plant or plantcell; (d) a plant or plant cell which is genetically identical to thesubject plant or plant cell but which is not exposed to the sametreatment (e.g., herbicide treatment) as the subject plant or plantcell; or (e) the subject plant or plant cell itself, under conditions inwhich the gene of interest is not expressed.

i. Hydroxyphenylpyruvate Dioxygenase Activity

As used herein, “hydroxyphenylpyruvate dioxygenase activity” or “HPPDactivity” refers to the conversion of 4-hydroxyphenylpyruvate tohomogentisate. As used herein, a polypeptide having “HPPD activity”comprises an HPPD polypeptide or an active variant or fragment thereofthat retains sufficient HPPD activity such that (i) when expressed atsufficient levels in a cell that requires HPPD activity for viability,the HPPD polypeptide or active variant or fragment exhibits sufficientHPPD activity to maintain viability of the cell in which it isexpressed; or (ii) when expressed in a cell that requires HPPD activityfor viability, the HPPD polypeptide, or active variant or fragmentthereof, when expressed in combination with one or more additional HPPDpolypeptides results in the viability of the cell. In one embodiment,the HPPD activity of an HPPD polypeptide, or an active variant orfragment thereof, is such that in the absence of an HPPD inhibitor saidpolypeptide or active variant or fragment thereof displays at leastabout 5%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%,75%, 80%, 85%, 90%, or 95% or greater of the HPPD activity displayed inany one of SEQ ID NO:2-83. Methods to determine such kinetic parameters(i.e., K_(m), k_(cat), k_(cat)/K_(m)) are known and discussed elsewhereherein.

In still further embodiments, the HPPD polypeptide or active variant orfragment thereof has an activity that is at least equivalent to a nativeHPPD polypeptide or has an activity that is increased when compared to anative HPPD polypeptide. An “equivalent” HPPD activity refers to anactivity level that is not statistically significantly different fromthe control as determined through any enzymatic kinetic parameter,including for example, via K_(m), k_(cat), or k_(cat)/K_(m). Anincreased HPPD activity comprises any statistically significant increasein HPPD activity as determined through any enzymatic kinetic parameter,such as, for example, K_(m), k_(cat), or k_(cat)/K_(m). In specificembodiments, an increase in HPPD activity comprises at least a 1.1, 1.2,1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 2, 3, 4, 5, 6, 7, 8, 9, or 10 fold orgreater improvement in a given kinetic parameter when compared to themaize wild-type HPPD sequence as set forth in SEQ ID NO:1 or whencompared to a native HPPD polypeptide. Methods to determine such kineticparameters are known.

Briefly, HPPD catalyzes the conversion of 4-hydroxyphenylpyruvate (HPP)to homogentisate. Substrate and product do not differ in absorbance oflight at any useful wavelength. However, homogentisate dioxygenase (HGD)catalyzes the conversion of homogentisate into maleylacetoacetate whichabsorbs strongly at 320 nm. Thus, by combining 4-hydroxyphenylpyruvatewith both HPPD and HGD under the appropriate reaction conditions HPPDactivity can be assayed.

As used herein, a “native” HPPD polypeptide comprises any wild-type HPPDsequence. Such sequences are known in the art, and representativenative/wild-type HPPD sequences from various monocot and dicot plantsare set forth in FIG. 4 and SEQ ID NO: 1. In specific embodiments, thebiologically active fragments and variants of the HPPD sequences iscompared to the maize wild-type HPPD polypeptide (SEQ ID NO: 1) or to anative HPPD polypeptide.

As used herein, a “corresponding native” HPPD polypeptide comprises thenative or wild type sequence from which the biologically active variantis derived. For example, for a biologically active variant or fragmentof a soy HPPD polypeptide, the corresponding native HPPD polypeptidewould be the native soy sequence as set forth in SEQ ID NO:100.

ii. Insensitivity to HPPD Inhibitors

In order to provide plants with tolerance to commercially usefulapplication rates of at least one desired HPPD inhibitor, it isadvantageous to use polynucleotides which encode HPPD polypeptideshaving sufficient HPPD activity and having an insensitivity toinhibition by at least one or more HPPD inhibitor. Thus, in specificembodiments, the HPPD polynucleotides and polypeptides and activevariants and fragments thereof provided herein display an increasedinsensitivity to an HPPD inhibitor when compared to a correspondingnative HPPD polypeptide and/or an increased insensitivity when comparedto the maize native HPPD polypeptide (SEQ ID NO: 1).

As used herein, an “HPPD inhibitor” comprises any compound orcombinations of compounds which decrease the ability of HPPD to catalyzethe conversion of 4-hydroxyphenylpyruvate to homogentisate. In specificembodiments, the HPPD inhibitor comprises a herbicidal inhibitor ofHPPD. Non-limiting examples of HPPD inhibitors include, triketones (suchas, mesotrione, sulcotrione, topramezone, and tembotrione); isoxazoles(such as, pyrasulfotole and isoxaflutole); pyrazoles (such as,benzofenap, pyrazoxyfen, and pyrazolynate); and benzobicyclon.Agriculturally acceptable salts of the various inhibitors include salts,the cations or anions of which are known and accepted in the art for theformation of salts for agricultural or horticultural use. See, forexample, International Publication No. WO 2005/053407 hereinincorporated by reference.

An “increased” or an “improved” insensitivity are used interchangeablyherein. An “increased” or an “improved” insensitivity to an HPPDinhibitor comprises any significant increase in the insensitivity of theHPPD polypeptide to the inhibitor as determined through any enzymatickinetic parameter, such as, for example, the dissociation constant(K_(D)) of the enzyme-inhibitor complex, the rates of association(k_(ON)), or dissociation (k_(OFF)) of inhibitor with or from enzyme, orthe ratio of k_(OFF)/k_(ON). This disclosure additionally definesparameters, “ON rate ratio”, “OFF rate ratio”, and “insensitivityparameter” that are not direct measurements of on and off rates but aremeasurements of the effect of the on and off rates inherent to aparticular HPPD enzyme on its catalytic function when the enzyme isexposed to the inhibitor. An improvement in insensitivity need not showan improvement in all kinetic parameters. The improvement of a singlekinetic parameter or any combination thereof is sufficient to classifythe change as an improvement in insensitivity. In specific embodiments,the increased insensitivity to the HPPD inhibitor is determined bymeasuring these novel insensitivity parameters of the enzyme. Thus, inspecific embodiments, the increased insensitivity to an HPPD inhibitorcomprises at least a 0.2, 0.3, 0.5, 0.7, 0.9, 1, 2, 3, 4, 5, 6, 7, 8, 9,10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 40, 50, 60, 70 fold orgreater improvement in a given kinetic parameter when compared to anative HPPD polypeptide and/or when compared to the maize wild-type HPPDsequence as set forth in SEQ ID NO:1.

In specific embodiments, an improved insensitivity to an HPPD inhibitorcomprises (a) a slower rate of association of enzyme and inhibitor asquantified, for example, by a higher ON rate ratio than native HPPD; (b)a faster rate of dissociation of inhibitor from enzyme as quantified,for example, by a higher OFF rate ratio than native HPPD; and/or (c)both a slower rate of association of inhibitor with enzyme and a fasterrate of dissociation of inhibitor from enzyme as quantified, forexample, by a higher product of ON rate ratio and OFF rate ratio thannative HPPD.

Methods to determine kinetic parameters for measuring the insensitivityof HPPD to an inhibitor are known. See also, Examples 1 and 4. Briefly,herbicidal inhibitors of HPPD form a tight complex with the enzyme bythe dual mechanisms of coordination to the active site iron atom througha pair of keto oxygens and a Pi stack of the aromatic ring of theinhibitor between a pair of active site phenylalanines. As a result,conventional I₅₀ determinations are not able to distinguish differencesin binding affinity among various forms of HPPD and the inhibitor. Allvalues will be the same, namely, 50% of the enzyme concentration. Todevise a parameter for detecting changes in inhibitor binding affinity,K_(D), one can utilize the relationship between K_(D) and the rates ofbinding and release of inhibitor (I) to and from the enzyme (E).

${E + I}\overset{k_{ON}}{\underset{k_{OFF}}{\rightleftarrows}}{EI}$At equilibrium, rates of binding and release are equal. Thus,k _(ON)[E][I]=k _(OFF)[EI]Written as a dissociation (products over reactants), the equation can bere-arranged to:

$\frac{\lbrack E\rbrack\lbrack I\rbrack}{\lbrack{EI}\rbrack} = {\frac{k_{OFF}}{k_{ON}} = K_{D}}$

Higher K_(D) (reduced affinity or increased insensitivity) can beattained with a numerically smaller ON rate, a larger OFF rate or both.To detect changes in ON and OFF rates, one can observe the time courseof an HPPD reaction as inhibitor binds to and inactivates the enzyme (ONrate), or is released from a pre-formed enzyme-inhibitor complex (OFFrate). See, for example, Example 1.

A quantitative indicator of ON rate can be obtained by monitoring thetime courses of HPPD reactions in the presence and absence of inhibitor(e.g. mesotrione). The ratio of the reaction rate with inhibitor to thatwithout inhibitor during the 70 to 90 second interval of the reaction isthe “ON rate ratio”.

A quantitative indicator of OFF rate can be obtained by observing thetime course of an HPPD reaction as the HPPD inhibitor (such asmesotrione) is released from a pre-formed enzyme-inhibitor complex.Reaction velocity accelerates as inhibitor is released from the enzymeuntil a steady state is reached, during which the reaction velocity isconstant. The ratio of the steady state rate in mixtures containingmesotrione (or other herbicidal inhibitor) to the initial velocity ofmixtures lacking inhibitor is termed the “OFF rate ratio”. Anotherparameter to record is the time span required for the reactions withinhibitor to reach the steady state. In still further embodiments, to besure that improvement in ON rates is being taken into account, the ONand OFF rate ratios are multiplied together and the product is termedthe “insensitivity parameter.”

The increased insensitivity of an HPPD inhibitor can also be determinedby assaying the increased insensitivity of a cell, a plant, a plant cellexpressing said HPPD polypeptide or active fragment or variant thereof.In such instances, the cell, plant, or plant cell expressing an HPPDsequence having an increased insensitivity to an HPPD inhibitor willdisplay an increased tolerance to the HPPD inhibitor or to a combinationof HPPD inhibitors when compared to a control cell, plant or plant cellnot expressing the HPPD sequence. “Increased tolerance” to a herbicideis demonstrated when plants which display the increased tolerance to aherbicide are subjected to the HPPD inhibitor and a dose/response curveis shifted to the right when compared with that provided by anappropriate control plant. Such dose/response curves have “dose” plottedon the x-axis and “percentage injury”, “herbicidal effect” etc. plottedon the y-axis. Plants which are substantially “resistant” or “tolerant”to the herbicide exhibit few, if any, bleached, necrotic, lytic,chlorotic or other lesions and are not stunted, wilted or deformed whensubjected to the herbicide at concentrations and rates which aretypically employed by the agricultural community to kill weeds in thefield.

For example, a plant expressing an HPPD polypeptide which displays anincreased insensitivity to an HPPD inhibitor will tolerate statisticallysignificantly higher levels of the HPPD inhibitor than a control plantnot expressing the HPPD polypeptide. In specific embodiments, a planttransfected and expressing one or more HPPD polypeptide sequencedisclosed herein, and the active variants and fragments thereof, allowfor an increased insensitivity to an HPPD inhibitor comprising, forexample, at least a 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16,17, 18, 19, 20, 100 fold or greater increase in a given performanceparameter when compared to untransformed plants. See, also, Examples 1for exemplary assays.

Different HPPD polypeptides can provide different levels of tolerance todifferent HPPD-inhibitor herbicides. While a given HPPD polypeptide mayprovide a useful level of tolerance to some HPPD-inhibitor herbicides itmay be quite inadequate to provide commercial levels of tolerance to adifferent HPPD-inhibitor herbicide which, for example, may control adifferent spectrum of weeds, be cheaper to make or offer environmentalbenefits. Thus, the various HPPD polypeptides disclosed herein can beused in combination in a single plant, plant explant or plant cell toexpand and/or improve the tolerance to a desired HPPD herbicide orcombination of HPPD herbicides.

B. Active Fragments and Variants of HPPD Sequences

Methods and compositions are provided which employ polynucleotides andpolypeptides having HPPD activity and having an insensitivity to atleast one HPPD inhibitor.

i. Polynucleotide and Polypeptide Fragments

Fragments and variants of HPPD polynucleotides and polypeptides are alsoencompassed by the present disclosure. By “fragment” is intended aportion of the polynucleotide or a portion of the amino acid sequenceand hence protein encoded thereby. Fragments of a polynucleotide mayencode protein fragments that retain HPPD activity and HPPD inhibitorinsensitivity. Alternatively, fragments of a polynucleotide that isuseful as hybridization probes generally do not encode fragment proteinsretaining biological activity. Thus, fragments of a nucleotide sequencemay range from at least about 20 nucleotides, about 50 nucleotides,about 100 nucleotides, about 150 nucleotides, and up to the full-lengthpolynucleotide encoding the HPPD polypeptides.

A fragment of an HPPD polynucleotide that encodes a biologically activeportion of an HPPD protein of the disclosure will encode at least 20,50, 75, 100, 150, 175, 200, 225, 250, 275, 300, 325, 350, 375, 400, 410,415, 420, 425, 430, 435, or 440 contiguous amino acids, or up to thetotal number of amino acids present in a full-length HPPD polypeptide.Fragments of an HPPD polynucleotide that are useful as hybridizationprobes or PCR primers generally need not encode a biologically activeportion of an HPPD protein.

Thus, a fragment of an HPPD polynucleotide may encode a biologicallyactive portion of an HPPD polypeptide, or it may be a fragment that canbe used as a hybridization probe or PCR primer using methods disclosedbelow. A biologically active portion of an HPPD polypeptide can beprepared by isolating a portion of one of the HPPD polynucleotides,expressing the encoded portion of the HPPD polypeptides (e.g., byrecombinant expression in vitro), and assessing the activity of the HPPDportion of the HPPD protein. Polynucleotides that are fragments of anHPPD nucleotide sequence comprise at least 16, 20, 50, 75, 100, 150,200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 800, 900, 1,000,1,100, 1,200, 1,300, or 1,400 contiguous nucleotides, or up to thenumber of nucleotides present in a full-length HPPD polynucleotidedisclosed herein.

In one embodiment, the HPPD polynucleotides and/or polypeptides compriseor encode an N-terminal truncation of the HPPD polypeptide. Such activeHPPD fragments comprise an N-terminal deletion of at least the first 1,2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21,22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39,40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, or more amino acids of theHPPD polypeptide of any one of SEQ ID NO:2-83. In specific embodiments,N-terminal deletions are designed to comprise a methionine residue onthe N-terminus. In specific embodiments, a fragment of the HPPDpolypeptide or polynucleotide comprising or encoding an N-terminaltruncated HPPD polypeptide comprises or encodes a polypeptide having adeletion of amino acids 2-23 of any one of SEQ ID NO:2-83.

ii. Polynucleotide and Polypeptide Variants

“Variant” protein is intended to mean a protein derived from a nativeprotein by deletion (i.e., truncation at the 5′ and/or 3′ end) and/or adeletion, or addition, of one or more amino acids at one or moreinternal sites in the native protein and/or substitution of one or moreamino acids at one or more sites in the native protein. Variant proteinsencompassed are biologically active, that is they continue to possessthe desired biological activity of the native protein, that is, haveHPPD activity and/or display insensitivity to a HPPD inhibitor asdescribed herein. Such variants may result from, for example, geneticpolymorphism or from human manipulation.

“Variants” is intended to mean substantially similar sequences. Forpolynucleotides, a variant comprises a polynucleotide having a deletion(i.e., truncations) at the 5′ and/or 3′ end and/or a deletion and/oraddition of one or more nucleotides at one or more internal sites withinthe native polynucleotide and/or a substitution of one or morenucleotides at one or more sites in the native polynucleotide. As usedherein, a “native” polynucleotide or polypeptide comprises a naturallyoccurring nucleotide sequence or amino acid sequence, respectively. Forpolynucleotides, conservative variants include those sequences that,because of the degeneracy of the genetic code, encode the amino acidsequence of one of the HPPD polypeptides of the disclosure. Naturallyoccurring variants such as these can be identified with the use ofwell-known molecular biology techniques, as, for example, withpolymerase chain reaction (PCR) and hybridization techniques as outlinedbelow. Variant polynucleotides also include synthetically derivedpolynucleotides, such as those generated, for example, by usingsite-directed mutagenesis or gene synthesis but which still encode anHPPD polypeptide.

Biologically active variants of an HPPD polypeptide (and thepolynucleotide encoding the same) will have at least about 90%, 91%,92%, 93%, 94%, 95%, 95.5%, 95.7%, 95.9%, 96%, 96.3%, 96.5%, 96.9%, 97%,97.3%, 97.5%, 97.9%, 98%, 98.3%, 98.5%, 98.9%, 99%, 99.3%, 99.5%, 99.6%or more sequence identity to the polypeptide of any one of SEQ IDNO:2-83.

In an aspect, biologically active variants of an HPPD polypeptide (andthe polynucleotide encoding the same) will have at least about 90%, 91%,92%, 93%, 94%, 95%, 95.5%, 95.7%, 95.9%, 96%, 96.3%, 96.5%, 96.9%, 97%,97.3%, 97.5%, 97.9%, 98%, 98.3%, 98.5%, 98.9%, 99%, 99.3%, 99.5%, 99.6%or more sequence identity to the polypeptide of any one of SEQ ID NO:4,7, 8, 18, and 18.

In other embodiments, variants of a HPPD polypeptides (andpolynucleotide encoding the same) will have at least about 90%, 91%,92%, 93%, 94%, 95%, 95.5%, 95.7%, 95.9%, 96%, 96.3%, 96.5%, 96.9%, 97%,97.3%, 97.5%, 97.9%, 98%, 98.3%, 98.5%, 98.9%, 99%, 99.3%, 99.5% or moresequence identity to an HPPD polypeptide having an N-terminal deletion.For example, such polypeptides comprise an N-terminal truncation of anyone of SEQ ID NO:2-83, comprising an N-terminal deletion of at least thefirst 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19,20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37,38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50 amino acids whereinsaid active variant of the HPPD polypeptide comprises at least 90%, 91%,92%, 93%, 94%, 95%, 95.5%, 95.7%, 95.9%, 96%, 96.3%, 96.5%, 96.9%, 97%,97.3%, 97.5%, 97.9%, 98%, 98.3%, 98.5%, 98.9%, 99%, 99.3%, 99.5% or moresequence identity to an N-terminal deletion of the HPPD polypeptide. Infurther embodiments, the N-terminal truncates further comprise amethionine amino acid residue on the N-terminus. In specificembodiments, fragments of the HPPD polypeptide have a deletion of aminoacids 2-23 of any one of SEQ ID NO:2-83. Thus, further provided are HPPDpolypeptides comprising at least 90%, 91%, 92%, 93%, 94%, 95%, 95.5%,95.7%, 95.9%, 96%, 96.3%, 96.5%, 96.9%, 97%, 97.3%, 97.5%, 97.9%, 98%,98.3%, 98.5%, 98.9%, 99%, 99.3%, 99.5% or more sequence identity to theamino acid sequence set forth in any one of SEQ ID NO:2-83.

In other embodiments, variants of a particular polypeptide (andpolynucleotide encoding the same) will have a bit score of at least 700,710, 720, 721, 722, 723, 724, 725, 726, 728, 729, 730, 731, 732, 733,734, 735, 736, 738, 739, 740, 741, 742, 743, 744, 745, 746, 747, 748,749, 750, 751, 752, 753, 754, 755, 756, 757, 758, 759, 760, 761, 762,763, 764, 765, 766, 767, 768, 769, 770, 771, 772, 773, 774, 775, 776,777, 778, 779, 780, 781, 782, 783, 784, 785, 786, 787, 788, 789, 790,791, 792, 793, 794, 795, 796, 797, 798, 799, 800, 801, 802, 803, 804,805, 806, 807, 808, 809, 810, 811, 812, 813, 814, 815, 816, 817, 818,819, 820, 821, 822, 823, 824, 825, 826, 828, 829, 830, 831, 832, 833,834, 835, 836, 838, 839, 840, 841, 842, 843, 844, 845, 846, 847, 848,849, 850, 851, 852, 853, 854, 855, 856, 857, 858, 859, 860, 861, 862,863, 864, 865, 866, 867, 868, 869, 870, 871, 872, 873, 874, 875, 876,877, 878, 879, 880, 881, 882, 883, 884, 885, 886, 887, 888, 889, 890 orgreater as determined by parameters described elsewhere herein to apolypeptide of any one of SEQ ID NO:2-83.

The HPPD polypeptide and the active variants and fragments thereof maybe altered in various ways including amino acid substitutions,deletions, truncations, and insertions. Methods for such manipulationsare generally known in the art. For example, amino acid sequencevariants and fragments of the HPPD proteins can be prepared by mutationsin the DNA. Methods for mutagenesis and polynucleotide alterations arewell known in the art. See, for example, Kunkel (1985) Proc. Natl. Acad.Sci. USA 82:488-492; Kunkel et al. (1987) Methods in Enzymol.154:367-382; U.S. Pat. No. 4,873,192; Walker and Gaastra, eds. (1983)Techniques in Molecular Biology (MacMillan Publishing Company, New York)and the references cited therein. Guidance as to appropriate amino acidsubstitutions that do not affect biological activity of the protein ofinterest may be found in the model of Dayhoff et al. (1978) Atlas ofProtein Sequence and Structure (Natl. Biomed. Res. Found., Washington,D.C.), herein incorporated by reference. Conservative substitutions,such as exchanging one amino acid with another having similarproperties, may be optimal.

Obviously, the mutations that will be made in the DNA encoding thevariant must not place the sequence out of reading frame and optimallywill not create complementary regions that could produce secondary mRNAstructure. See, EP Patent Application Publication No. 75,444.

Variant polynucleotides and proteins also encompass sequences andproteins derived from a mutagenic and recombinogenic procedure such asDNA shuffling. With such a procedure, one or more different HPPD codingsequences can be manipulated to create a new HPPD possessing the desiredproperties. In this manner, libraries of recombinant polynucleotides aregenerated from a population of related sequence polynucleotidescomprising sequence regions that have substantial sequence identity andcan be homologously recombined in vitro or in vivo. For example, usingthis approach, sequence motifs encoding a domain of interest may beshuffled between the HPPD sequences disclosed herein and other knownHPPD genes to obtain a new gene coding for a protein with an improvedproperty of interest, such as a decreased K_(m) in the case of anenzyme. Strategies for such DNA shuffling are known in the art. See, forexample, Stemmer (1994) Proc. Natl. Acad. Sci. USA 91:10747-10751;Stemmer (1994) Nature 370:389-391; Crameri et al. (1997) Nature Biotech.15:436-438; Moore et al. (1997) J. Mol. Biol. 272:336-347; Zhang et al.(1997) Proc. Natl. Acad. Sci. USA 94:4504-4509; Crameri et al. (1998)Nature 391:288-291; and U.S. Pat. Nos. 5,605,793 and 5,837,458.

In still further embodiments, the HPPD polypeptide or active variantsand fragments thereof have been modified to remove one or more sequencesthat are present in other proteins which are allergens. As used herein,a “matching sequence” comprises a region of 8 contiguous identical aminoacids present in a known protein allergen. See, for example, Ladics(2008) Food and Chemical Toxicology 46: S20-S23, herein incorporated byreference. Such identified 8-amino acid sequences, however, do notnecessarily have any allergenic potential or confer allergenicity.Nonetheless, to comply with established criteria governing the potentialfor allergenic cross-reactivity (FAO/WHO 2001, Codex 2003), the matchingsequences can be altered so the resulting polypeptide no longer containsthe 8 residue contiguous match. Identification of such matchingsequences is done by comparing the predicted amino acid sequence of thetransgene product with that of a database of known or putative proteinallergens and subsequently altering the identified amino acid sequenceto remove the allergenic match. The database utilized for this analysiswas the AllergenOnline database of known protein allergens housed at theUniversity of Nebraska (www.allergenonline.org). It is recognized thatin specific embodiments, removal of the matching sequence viasubstitution, deletion and/or addition of amino acids will not impactthe HPPD activity or the HPPD inhibitor insensitivity of the proteinwhen compared to an appropriate control. TAAAAGAA (amino acids 6-13 inmaize wild-type HPPD SEQ ID NO:1) was changed to TATAAGAA (SEQ IDNO:101) to eliminate the 8 amino acid match to an allergen sequence inthe database. Such a change does not alter the activity or insensitivityto herbicides of HPPD enzymes. See, for example, Codex AlimentariusCommission, Alinorm 03/34: Joint FAO/WHO Food Standard Programme, CodexAlimentarius Commission, Twenty-Fifth Session, Rome, Italy, Jun. 30-Jul.5, 2003. Appendix III, Guideline for the conduct of food safetyassessment of foods derived from recombinant-DNA plants, and AppendixIV, Annex of the assessment of possible allergenicity, 47-60 andFAO/WHO, 2001. Evaluation of allergenicity of genetically modifiedfoods. Report of a Joint FAO/WHO Expert Consultation on Allergenicity ofFoods Derived from Biotechnology. Jan. 22-25, 2001. Rome, Italy.

C. Chloroplast Transit Peptides

Further provided are various methods and compositions which compriseHPPD polypeptides and active variants and fragments thereof, andpolynucleotides encoding the same, wherein the HPPD sequence comprises achloroplast transit peptide. As used herein, the term “chloroplasttransit peptide” will be abbreviated “CTP” and refers to the N-terminalportion of a chloroplast precursor protein that directs the latter intochloroplasts and is subsequently cleaved off by the chloroplastprocessing protease. When a CTP is operably linked to the N-terminus ofa polypeptide, the polypeptide is translocated into the chloroplast.Removal of the CTP from a native protein reduces or abolishes theability of the native protein from being transported into thechloroplast. An operably linked chloroplast transit peptide is found atthe N-terminus of the protein to be targeted to the chloroplast and islocated upstream and immediately adjacent to the transit peptidecleavage site that separates the transit peptide from the mature proteinto be targeted to the chloroplast.

The term “chloroplast transit peptide cleavage site” refers to a sitebetween two amino acids in a chloroplast-targeting sequence at which thechloroplast processing protease acts. Chloroplast transit peptidestarget the desired protein to the chloroplast and can facilitate theproteins translocation into the organelle. This is accompanied by thecleavage of the transit peptide from the mature polypeptide or proteinat the appropriate transit peptide cleavage site by a chloroplastprocessing protease, native to the chloroplast. Accordingly, achloroplast transit peptide further comprises a suitable cleavage sitefor the correct processing of the pre-protein to the mature polypeptidecontained within the chloroplast.

Thus, any one of the polypeptides, or the polynucleotide encoding thesame, or active variants and fragments thereof set forth in any one ofSEQ ID NO:2-83, and biologically active variants and fragments thereof,can comprise a heterologous CTP sequence. Additional CTPs from HPPDpolypeptides can be employed (see for example, PCT Publication No. WO2012/021797, entitled “Methods and Compositions for Targeting Sequencesof Interest to a Chloroplast.”).

In still further embodiments, an HPPD polypeptide, and a polynucleotideencoding the same, is provided, wherein the HPPD polypeptide comprises aheterologous chloroplast transit peptide that is not from the wild-typemaize HPPD polypeptide or an active variant or fragment thereof. Suchheterologous chloroplast transit peptides are known, including but notlimited to those derived from Pisum (JP 1986224990; E00977), carrot (Luoet al. (1997) Plant Mol. Biol., 33 (4), 709-722 (Z33383), Nicotiana(Bowler et al., EP 0359617; A09029), Oryza (de Pater et al. (1990) PlantMol. Biol., 15 (3), 399-406 (X51911), as well as synthetic sequencessuch as those provided in EP 0189707; U.S. Pat. Nos. 5,728,925;5,717,084 (A10396 and A10398). In one embodiment, the heterologouschloroplast transit peptide is from the ribulose-1,5-bisphosphatecarboxylase (Rubisco) small subunit precursor protein isolated from anyplant. The Rubisco small subunit is well characterized from a variety ofplants and the transit peptide from any of them are suitable for use inthe compositions and methods of the present disclosure. See for example,Physcomitrella (Quatrano et al., AW599738); Lotus (Poulsen et al.,AW428760); Citrullus (J. S. Shin, AI563240); Nicotiana (Appleby et al.(1997) Heredity 79(6), 557-563); alfalfa (Khoudi et al. (1997) Gene,197(1/2), 343-351); potato and tomato (Fritz et al. (1993) Gene, 137(2),271-4); wheat (Galili et al. (1991) Theor. Appl. Genet. 81(1), 98-104);and rice (Xie et al. (1987) Sci. Sin., Ser. B (Engl. Ed.), 30(7),706-19). For example, transit peptides may be derived from the Rubiscosmall subunit isolated from plants including but not limited to,soybean, rapeseed, sunflower, cotton, corn, tobacco, alfalfa, wheat,barley, oats, sorghum, rice, Arabidopsis, sugar beet, sugar cane,canola, millet, beans, peas, rye, flax, and forage grasses. In anaspect, methods and compositions of the present disclosure can utilizethe Rubisco small subunit precursor protein from, for example,Arabidopsis or tobacco.

In other embodiments, the HPPD polypeptides and active variants andfragments thereof, and polynucleotide encoding the same, do not comprisea CTP. In such instances, the HPPD polypeptide and active variants andfragments thereof, or polynucleotides encoding the same, do not comprisea chloroplast transit peptide. Such polypeptides can be expressed in thecytoplasm of a plant, plant cell or explant and still conferinsensitivity of the cell, plant or plant cell to an HPPD inhibitor. Instill other embodiments, the HPPD polynucleotides lacking thechloroplast transit peptide are introduced directly into the chloroplastvia chloroplast transformation. Such methods of chloroplasttransformation are discussed in detail elsewhere herein.

Thus, further provided herein are HPPD polynucleotides and polypeptidesand variants and fragments thereof that have HPPD activity and displayinsensitivity to an HPPD inhibitor and lack a chloroplast transitpeptide. Various N-terminal truncations are described elsewhere herein.

In other embodiments, the HPPD polypeptide or polynucleotide encodingthe same, lacks the first 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 0.37,38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50 or more aminoacids of any one of SEQ ID NO: 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14,15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32,33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50,51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 74, 65, 66, 67, 68,69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86,87, 88, 89, 90, 61, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103,104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117,118, 119, 120, 121, 212, 123, 124, 125, 126, 127, 128, 129, 130, 131,132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145,146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159,160, 161, 162, 163, 164, 383, 384, 385, 386, 387, 388, 389, 404, 405,406, 407, 408, 409, 410, 411, 412, 413, 414, 415, 416, 417, 418, 419,420, 421, 422, 423, 424, 425, 426, 427, 428, 429, 430, 458, or 459 orbiologically active variant or fragment thereof. In specificembodiments, the sequence set forth in any one of SEQ ID NO:2-83, andbiologically active variants and fragments thereof, or thepolynucleotide encoding the same, lack the first the 2-23 amino acid ofthe corresponding SEQ ID NO.

D. Sequence Comparisons

The following terms are used to describe the sequence relationshipsbetween two or more polynucleotides or polypeptides: (a) “referencesequence”, (b) “comparison window”, (c) “sequence identity”, and, (d)“percent sequence identity.”

(a) As used herein, “reference sequence” is a defined sequence used as abasis for sequence comparison. A reference sequence may be a subset orthe entirety of a specified sequence; for example, as a segment of afull-length cDNA or gene sequence, or the complete cDNA or gene sequenceor protein sequence.

(b) As used herein, “comparison window” makes reference to a contiguousand specified segment of a polypeptide sequence, wherein the polypeptidesequence in the comparison window may comprise additions or deletions(i.e., gaps) compared to the reference sequence (which does not compriseadditions or deletions) for optimal alignment of the two polypeptides.Generally, the comparison window is at least 5, 10, 15, or 20 contiguousamino acid in length, or it can be 30, 40, 50, 100, or longer. Those ofskill in the art understand that to avoid a high similarity to areference sequence due to inclusion of gaps in the polypeptide sequencea gap penalty is typically introduced and is subtracted from the numberof matches.

Methods of alignment of sequences for comparison are well known in theart. Thus, the determination of percent sequence identity between anytwo sequences can be accomplished using a mathematical algorithm.Non-limiting examples of such mathematical algorithms are the algorithmof Myers and Miller (1988) CABIOS 4:11-17; the local alignment algorithmof Smith et al. (1981) Adv. Appl. Math. 2:482; the global alignmentalgorithm of Needleman and Wunsch (1970) J. Mol. Biol. 48:443-453; thesearch-for-local alignment method of Pearson and Lipman (1988) Proc.Natl. Acad. Sci. 85:2444-2448; the algorithm of Karlin and Altschul(1990) Proc. Natl. Acad. Sci. USA 872264, modified as in Karlin andAltschul (1993) Proc. Natl. Acad. Sci. USA 90:5873-5877.

Computer implementations of these mathematical algorithms can beutilized for comparison of sequences to determine sequence identity.Such implementations include, but are not limited to: CLUSTAL in thePC/Gene program (available from Intelligenetics, Mountain View, Calif.);the ALIGN program (Version 2.0) and GAP, BESTFIT, BLAST, FASTA, andTFASTA in the GCG Wisconsin Genetics Software Package, Version 10(available from Accelrys Inc., 9685 Scranton Road, San Diego, Calif.,USA). Alignments using these programs can be performed using the defaultparameters. The CLUSTAL program is well described by Higgins et al.(1988) Gene 73:237-244 (1988); Higgins et al. (1989) CABIOS 5:151-153;Corpet et al. (1988) Nucleic Acids Res. 16:10881-90; Huang et al. (1992)CABIOS 8:155-65; and Pearson et al. (1994) Meth. Mol. Biol. 24:307-331.The ALIGN program is based on the algorithm of Myers and Miller (1988)supra. A PAM120 weight residue table, a gap length penalty of 12, and agap penalty of 4 can be used with the ALIGN program when comparing aminoacid sequences. The BLAST programs of Altschul et al (1990) J. Mol.Biol. 215:403 are based on the algorithm of Karlin and Altschul (1990)supra. BLAST nucleotide searches can be performed with the BLASTNprogram, score=100, wordlength=12, to obtain nucleotide sequenceshomologous to a nucleotide sequence encoding a protein of the presentdisclosure. BLAST protein searches can be performed with the BLASTXprogram, score=50, wordlength=3, to obtain amino acid sequenceshomologous to a protein or polypeptide of the present disclosure. BLASTPprotein searches can be performed using default parameters. For example,see blast.ncbi.nlm.nih.gov/Blast.cgi.

To obtain gapped alignments for comparison purposes, Gapped BLAST (inBLAST 2.0) can be utilized as described in Altschul et al. (1997)Nucleic Acids Res. 25:3389. Alternatively, PSI-BLAST (in BLAST 2.0) canbe used to perform an iterated search that detects distant relationshipsbetween molecules. See Altschul et al. (1997) supra. When utilizingBLAST, Gapped BLAST, or PSI-BLAST, the default parameters of therespective programs (e.g., BLASTN for nucleotide sequences, BLASTP forproteins) can be used. See www.ncbi.nlm.nih.gov. Alignment may also beperformed manually by inspection.

In one embodiment, sequence identity/similarity values provided hereinrefer to the value obtained using GAP Version 10 using the followingparameters: % identity and % similarity for an amino acid sequence usingGAP Weight of 8 and Length Weight of 2, and the BLOSUM62 scoring matrix;or any equivalent program thereof. By “equivalent program” is intendedany sequence comparison program that, for any two sequences in question,generates an alignment having identical nucleotide or amino acid residuematches and an identical percent sequence identity when compared to thecorresponding alignment generated by GAP Version 10.

GAP uses the algorithm of Needleman and Wunsch (1970) J. Mol. Biol.48:443-453, to find the alignment of two complete sequences thatmaximizes the number of matches and minimizes the number of gaps. GAPconsiders all possible alignments and gap positions and creates thealignment with the largest number of matched bases and the fewest gaps.It allows for the provision of a gap creation penalty and a gapextension penalty in units of matched bases. GAP must make a profit ofgap creation penalty number of matches for each gap it inserts. If a gapextension penalty greater than zero is chosen, GAP must, in addition,make a profit for each gap inserted of the length of the gap times thegap extension penalty. Default gap creation penalty values and gapextension penalty values in Version 10 of the GCG Wisconsin GeneticsSoftware Package for protein sequences are 8 and 2, respectively. Fornucleotide sequences the default gap creation penalty is 50 while thedefault gap extension penalty is 3. The gap creation and gap extensionpenalties can be expressed as an integer selected from the group ofintegers consisting of from 0 to 200. Thus, for example, the gapcreation and gap extension penalties can be 0, 1, 2, 3, 4, 5, 6, 7, 8,9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65 or greater.

GAP presents one member of the family of best alignments. There may bemany members of this family, but no other member has a better quality.GAP displays four figures of merit for alignments: Quality, Ratio,Identity, and Similarity. The Quality is the metric maximized in orderto align the sequences. Ratio is the quality divided by the number ofbases in the shorter segment. Percent Identity is the percent of thesymbols that actually match. Percent Similarity is the percent of thesymbols that are similar. Symbols that are across from gaps are ignored.A similarity is scored when the scoring matrix value for a pair ofsymbols is greater than or equal to 0.50, the similarity threshold. Thescoring matrix used in Version 10 of the GCG Wisconsin Genetics SoftwarePackage is BLOSUM62 (see Henikoff and Henikoff (1989) Proc. Natl. Acad.Sci. USA 89:10915).

(c) As used herein, “sequence identity” or “identity” in the context oftwo polynucleotides or polypeptide sequences makes reference to theresidues in the two sequences that are the same when aligned for maximumcorrespondence over a specified comparison window. When percentage ofsequence identity is used in reference to proteins it is recognized thatresidue positions which are not identical often differ by conservativeamino acid substitutions, where amino acid residues are substituted forother amino acid residues with similar chemical properties (e.g., chargeor hydrophobicity). When sequences differ in conservative substitutions,the percent sequence identity may be adjusted upwards to correct for theconservative nature of the substitution. Sequences that differ by suchconservative substitutions are said to have “sequence similarity” or“similarity”. Means for making this adjustment are well known to thoseof skill in the art. Typically this involves scoring a conservativesubstitution as a partial rather than a full mismatch, therebyincreasing the percent sequence identity. Thus, for example, where anidentical amino acid is given a score of 1 and a non-conservativesubstitution is given a score of zero, a conservative substitution isgiven a score between zero and 1. The scoring of conservativesubstitutions is calculated, e.g., as implemented in the program PC/GENE(Intelligenetics, Mountain View, Calif.).

(d) As used herein, “percent sequence identity” means the valuedetermined by comparing two optimally aligned sequences over acomparison window, wherein the portion of the polynucleotide sequence inthe comparison window may comprise additions or deletions (i.e., gaps)as compared to the reference sequence (which does not comprise additionsor deletions) for optimal alignment of the two sequences. The percentageis calculated by determining the number of positions at which theidentical nucleic acid base or amino acid residue occurs in bothsequences to yield the number of matched positions, dividing the numberof matched positions by the total number of positions in the window ofcomparison, and multiplying the result by 100 to yield the percentsequence identity.

(e) Two sequences are “optimally aligned” when they are aligned forsimilarity scoring using a defined amino acid substitution matrix (e.g.,BLOSUM62), gap existence penalty and gap extension penalty so as toarrive at the highest score possible for that pair of sequences. Aminoacids substitution matrices and their use in quantifying the similaritybetween two sequences are well-known in the art and described, e.g., inDayhoff et al. (1978) “A model of evolutionary change in proteins.” In“Atlas of Protein Sequence and Structure,” Vol. 5, Suppl. 3 (ed. M. O.Dayhoff), pp. 345-352. Natl. Biomed. Res. Found., Washington, D.C. andHenikoff et al. (1992) Proc. Natl. Acad. Sci. USA 89:10915-10919. TheBLOSUM62 matrix (FIG. 10) is often used as a default scoringsubstitution matrix in sequence alignment protocols such as Gapped BLAST2.0. The gap existence penalty is imposed for the introduction of asingle amino acid gap in one of the aligned sequences, and the gapextension penalty is imposed for each additional empty amino acidposition inserted into an already opened gap. The gap existence penaltyis imposed for the introduction of a single amino acid gap in one of thealigned sequences, and the gap extension penalty is imposed for eachadditional empty amino acid position inserted into an already openedgap. The alignment is defined by the amino acids positions of eachsequence at which the alignment begins and ends, and optionally by theinsertion of a gap or multiple gaps in one or both sequences, so as toarrive at the highest possible score. While optimal alignment andscoring can be accomplished manually, the process is facilitated by theuse of a computer-implemented alignment algorithm, e.g., gapped BLAST2.0, described in Altschul et al, (1997) Nucleic Acids Res.25:3389-3402, and made available to the public at the National Centerfor Biotechnology Information Website (http://www.ncbi.nlm.nih.gov).Optimal alignments, including multiple alignments, can be preparedusing, e.g., PSI-BLAST, available through http://www.ncbi.nlm.nih.govand described by Altschul et al, (1997) Nucleic Acids Res. 25:3389-3402.

As used herein, similarity score and bit score is determined employingthe BLAST alignment used the BLOSUM62 substitution matrix, a gapexistence penalty of 11, and a gap extension penalty of 1. For the samepair of sequences, if there is a numerical difference between the scoresobtained when using one or the other sequence as query sequences, agreater value of similarity score is selected.

E. Plants

Plants, plant cells, plant parts, explants, seeds, and grain having theHPPD sequences disclosed herein are provided. In specific embodiments,the plants and/or plant parts have stably incorporated at least oneheterologous HPPD polypeptide disclosed herein or an active variant orfragment thereof. Thus, plants, plant cells, plant parts and seed areprovided which comprise at least one heterologous HPPD sequence of anyone of SEQ ID NO:2-83, and biologically active variants and fragmentsthereof, or any one of other variants disclosed herein, or abiologically active fragment and/or variant of the HPPD sequence. Inspecific embodiments, the HPPD sequences are characterized as havingHPPD activity and having an insensitivity to an HPPD inhibitor.

Further provided are plants, plant cells, plant parts, explants, seeds,and grain having the HPPD sequences having a heterologous CTP asdiscussed elsewhere herein. In light of employing HPPDs with and withoutCTP sequences, the term “stably incorporated” in a plant, plant cell,plant part, explant, seed, or grain refers to the integration of thepolynucleotide into the genomic DNA or to the integration of thepolynucleotide into the genome of a plastid (i.e., the chloroplast,amyloplasts, chromoplasts, statoliths, leucoplasts, elaioplasts, andproteinoplasts).

In specific embodiments, the heterologous polynucleotide in the plant orplant part is operably linked to a constitutive, tissue-preferred, orother promoter for expression in plants.

As used herein, the term “plant” includes immature or mature wholeplant, including a plant from which seed, grain, or anthers have beenremoved, as well as plant cells, plant protoplasts, plant cell tissuecultures from which plants can be regenerated, plant calli, plantclumps, and plant cells that are intact in plants or parts of plantssuch as embryos, pollen, ovules, seeds, leaves, flowers, branches,fruit, kernels, ears, cobs, husks, stalks, roots, root tips, anthers,and the like.

As used herein, “grain” is intended to mean the mature seed produced bycommercial growers for purposes other than growing or reproducing thespecies. Progeny, variants, and mutants of the regenerated plants arealso included within the scope of the disclosure, provided that theseparts comprise introduced polynucleotides encoding a disclosed HPPDpolypeptide.

As used herein, the term “plant part” or “plant parts” refers to anyplant part whether part of an intact living or growing plant or whetherisolated or separated from an intact living plant. Plant part includes,but is not limited, to protoplasts, leaves, stems, roots, root tips,anthers, pistils, seed, grain, embryo, pollen, ovules, cotyledon,hypocotyl, pod, flower, shoot, tissue, petiole, cells, meristematiccells, and the like.

As used herein, “explant” refers to plant tissue that is directlyexcised from an intact plant, such as a leaf, petal, sepal, stamen,filament anther, root, or stem.

The HPPD sequences and active variants and fragments thereof disclosedherein may be used for transformation of any plant species, including,but not limited to, monocots and dicots. Examples of plant species ofinterest include, but are not limited to, corn (Zea mays), Brassica sp.(e.g., B. napus, B. rapa, B. juncea), particularly those Brassicaspecies useful as sources of seed oil, alfalfa (Medicago sativa), rice(Oryza sativa), rye (Secale cereale), sorghum (Sorghum bicolor, Sorghumvulgare), millet (e.g., pearl millet (Pennisetum glaucum), proso millet(Panicum miliaceum), foxtail millet (Setaria italica), finger millet(Eleusine coracana)), sunflower (Helianthus annuus), safflower(Carthamus tinctorius), wheat (Triticum aestivum), soybean (Glycinemax), tobacco (Nicotiana tabacum), potato (Solanum tuberosum), peanuts(Arachis hypogaea), cotton (Gossypium barbadense, Gossypium hirsutum),sweet potato (Ipomoea batatus), cassava (Manihot esculenta), coffee(Coffea spp.), coconut (Cocos nucifera), pineapple (Ananas comosus),citrus trees (Citrus spp.), cocoa (Theobroma cacao), tea (Camelliasinensis), banana (Musa spp.), avocado (Persea americana), fig (Ficuscasica), guava (Psidium guajava), mango (Mangifera indica), olive (Oleaeuropaea), papaya (Carica papaya), cashew (Anacardium occidentale),macadamia (Macadamia integrifolia), almond (Prunus amygdalus), sugarbeets (Beta vulgaris), sugarcane (Saccharum spp.), oats, barley,vegetables, ornamentals, and conifers.

Vegetables include tomatoes (Lycopersicon esculentum), lettuce (e.g.,Lactuca sativa), green beans (Phaseolus vulgaris), lima beans (Phaseoluslimensis), peas (Lathyrus spp.), and members of the genus Cucumis suchas cucumber (C. sativus), cantaloupe (C. cantalupensis), and musk melon(C. melo). Ornamentals include azalea (Rhododendron spp.), hydrangea(Macrophylla hydrangea), hibiscus (Hibiscus rosasanensis), roses (Rosaspp.), tulips (Tulipa spp.), daffodils (Narcissus spp.), petunias(Petunia hybrida), carnation (Dianthus caryophyllus), poinsettia(Euphorbia pulcherrima), and chrysanthemum.

Conifers that may be employed in practicing methods of the presentdisclosure include, for example, pines such as loblolly pine (Pinustaeda), slash pine (Pinus elliotii), ponderosa pine (Pinus ponderosa),lodgepole pine (Pinus contorta), and Monterey pine (Pinus radiata);Douglas-fir (Pseudotsuga menziesii); Western hemlock (Tsuga canadensis);Sitka spruce (Picea glauca); redwood (Sequoia sempervirens); true firssuch as silver fir (Abies amabilis) and balsam fir (Abies balsamea); andcedars such as Western red cedar (Thuja plicata) and Alaska yellow-cedar(Chamaecyparis nootkatensis), and Poplar and Eucalyptus. In specificembodiments, plants of the present disclosure are crop plants (forexample, corn, alfalfa, sunflower, Brassica, soybean, cotton, safflower,peanut, sorghum, wheat, millet, tobacco, etc.). In other embodiments,corn and soybean plants are optimal, and in yet other embodiments cornplants are optimal.

Other plants of interest include grain plants that provide seeds ofinterest, oil-seed plants, and leguminous plants. Seeds of interestinclude grain seeds, such as corn, wheat, barley, rice, sorghum, rye,etc. Oil-seed plants include cotton, soybean, safflower, sunflower,Brassica, maize, alfalfa, palm, coconut, etc. Leguminous plants includebeans and peas. Beans include guar, locust bean, fenugreek, soybean,garden beans, cowpea, mungbean, lima bean, fava bean, lentils, chickpea,etc.

A “subject plant or plant cell” is one in which genetic alteration, suchas transformation, has been affected as to a gene of interest, or is aplant or plant cell which is descended from a plant or cell so alteredand which comprises the alteration. A “control” or “control plant” or“control plant cell” provides a reference point for measuring changes inphenotype of the subject plant or plant cell.

A control plant or plant cell may comprise, for example: (a) a wild-typeplant or cell, i.e., of the same genotype as the starting material forthe genetic alteration which resulted in the subject plant or cell; (b)a plant or plant cell of the same genotype as the starting material butwhich has been transformed with a null construct (i.e. with a constructwhich has no known effect on the trait of interest, such as a constructcomprising a marker gene); (c) a plant or plant cell which is anon-transformed segregant among progeny of a subject plant or plantcell; (d) a plant or plant cell genetically identical to the subjectplant or plant cell but which is not exposed to conditions or stimulithat would induce expression of the gene of interest; or (e) the subjectplant or plant cell itself, under conditions in which the gene ofinterest is not expressed.

F. Polynucleotide Constructs

The use of the term “polynucleotide” is not intended to limit thepresent disclosure to polynucleotides comprising DNA. Those of ordinaryskill in the art will recognize that polynucleotides can compriseribonucleotides and combinations of ribonucleotides anddeoxyribonucleotides. Such deoxyribonucleotides and ribonucleotidesinclude both naturally occurring molecules and synthetic analogues. Thepolynucleotides of the disclosure also encompass all forms of sequencesincluding, but not limited to, single-stranded forms, double-strandedforms, hairpins, stem-and-loop structures, and the like.

The HPPD polynucleotides disclosed herein can be provided in expressioncassettes for expression in the plant of interest. The cassette caninclude 5′ and 3′ regulatory sequences operably linked to an HPPDpolynucleotide or active variant or fragment thereof. “Operably linked”is intended to mean a functional linkage between two or more elements.For example, an operable linkage between a polynucleotide of interestand a regulatory sequence (i.e., a promoter) is a functional link thatallows for expression of the polynucleotide of interest. Operably linkedelements may be contiguous or non-contiguous. When used to refer to thejoining of two protein coding regions, by operably linked is intendedthat the coding regions are in the same reading frame. The cassette mayadditionally contain at least one additional gene to be cotransformedinto the organism. Alternatively, the additional gene(s) can be providedon multiple expression cassettes. Such an expression cassette isprovided with a plurality of restriction sites and/or recombinationsites for insertion of the HPPD polynucleotide or active variant orfragment thereof to be under the transcriptional regulation of theregulatory regions. The expression cassette may additionally containselectable marker genes.

The expression cassette can include in the 5′-3′ direction oftranscription, a transcriptional and translational initiation region(i.e., a promoter), an HPPD polynucleotide or active variant or fragmentthereof, and a transcriptional and translational termination region(i.e., termination region) functional in plants. The regulatory regions(i.e., promoters, transcriptional regulatory regions, and translationaltermination regions) and/or the HPPD polynucleotide or active variant orfragment thereof may be native/analogous to the host cell or to eachother. Alternatively, the regulatory regions and/or the HPPDpolynucleotide of or active variant or fragment thereof may beheterologous to the host cell or to each other. As discussed in furtherdetail elsewhere herein, the expression cassette can comprises achimeric polynucleotide comprising a heterologous CTP operably linked toan HPPD polynucleotide.

As used herein, “heterologous” in reference to a sequence is a sequencethat originates from a foreign species, or, if from the same species, issubstantially modified from its native form in composition and/orgenomic locus by deliberate human intervention. For example, a promoteroperably linked to a heterologous polynucleotide is from a speciesdifferent from the species from which the polynucleotide was derived,or, if from the same/analogous species, one or both are substantiallymodified from their original form and/or genomic locus, or the promoteris not the native promoter for the operably linked polynucleotide.

While it may be optimal to express the sequences using heterologouspromoters, the native promoter sequences may be used. Such constructscan change expression levels of the HPPD polynucleotide in the plant orplant cell. Thus, the phenotype of the plant or plant cell can bealtered.

The termination region may be native with the transcriptional initiationregion, may be native with the operably linked HPPD polynucleotide oractive variant or fragment thereof, may be native with the plant host,or may be derived from another source (i.e., foreign or heterologous) tothe promoter, the HPPD polynucleotide or active fragment or variantthereof, the plant host, or any combination thereof. Convenienttermination regions are available from the Ti-plasmid of A. tumefaciens,such as the octopine synthase and nopaline synthase termination regions.See also Guerineau et al. (1991) Mol. Gen. Genet. 262:141-144; Proudfoot(1991) Cell 64:671-674; Sanfacon et al. (1991) Genes Dev. 5:141-149;Mogen et al. (1990) Plant Cell 2:1261-1272; Munroe et al. (1990) Gene91:151-158; Ballas et al. (1989) Nucleic Acids Res. 17:7891-7903; andJoshi et al. (1987) Nucleic Acids Res. 15:9627-9639.

Where appropriate, the polynucleotides may be optimized for increasedexpression in the transformed plant. That is, the polynucleotides can besynthesized using plant-preferred codons for improved expression. See,for example, Campbell and Gowri (1990) Plant Physiol. 92:1-11 for adiscussion of host-preferred codon usage. Methods are available in theart for synthesizing plant-preferred genes. See, for example, U.S. Pat.Nos. 5,380,831, and 5,436,391, and Murray et al. (1989) Nucleic AcidsRes. 17:477-498, herein incorporated by reference.

Additional sequence modifications are known to enhance gene expressionin a cellular host. These include elimination of sequences encodingspurious polyadenylation signals, exon-intron splice site signals,transposon-like repeats, and other such well-characterized sequencesthat may be deleterious to gene expression. The G-C content of thesequence may be adjusted to levels average for a given cellular host, ascalculated by reference to known genes expressed in the host cell. Whenpossible, the sequence is modified to avoid predicted hairpin secondarymRNA structures.

The expression cassettes may additionally contain 5′ leader sequences.Such leader sequences can act to enhance translation. Translationleaders are known in the art and include: picornavirus leaders, forexample, EMCV leader (Encephalomyocarditis 5′ noncoding region)(Elroy-Stein et al. (1989) Proc. Natl. Acad. Sci. USA 86:6126-6130);potyvirus leaders, for example, TEV leader (Tobacco Etch Virus) (Gallieet al. (1995) Gene 165(2):233-238), MDMV leader (Maize Dwarf MosaicVirus) (Virology 154:9-20), and human immunoglobulin heavy-chain bindingprotein (BiP) (Macejak et al. (1991) Nature 353:90-94); untranslatedleader from the coat protein mRNA of alfalfa mosaic virus (AMV RNA 4)(Jobling et al. (1987) Nature 325:622-625); tobacco mosaic virus leader(TMV) (Gallie et al. (1989) in Molecular Biology of RNA, ed. Cech (Liss,New York), pp. 237-256); and maize chlorotic mottle virus leader (MCMV)(Lommel et al. (1991) Virology 81:382-385. See also, Della-Cioppa et al.(1987) Plant Physiol. 84:965-968.

In preparing the expression cassette, the various DNA fragments may bemanipulated, so as to provide for the DNA sequences in the properorientation and, as appropriate, in the proper reading frame. Towardthis end, adapters or linkers may be employed to join the DNA fragmentsor other manipulations may be involved to provide for convenientrestriction sites, removal of superfluous DNA, removal of restrictionsites, or the like. For this purpose, in vitro mutagenesis, primerrepair, restriction, annealing, resubstitutions, e.g., transitions andtransversions, may be involved.

A number of promoters can be used to express the various HPPD sequencedisclosed herein, including the native promoter of the polynucleotidesequence of interest. The promoters can be selected based on the desiredoutcome. Such promoters include, for example, constitutive,tissue-preferred, or other promoters for expression in plants.

Constitutive promoters include, for example, the core promoter of theRsyn7 promoter and other constitutive promoters disclosed in WO 99/43838and U.S. Pat. No. 6,072,050; the core CaMV 35S promoter (Odell et al.(1985) Nature 313:810-812); rice actin (McElroy et al. (1990) Plant Cell2:163-171); ubiquitin (Christensen et al. (1989) Plant Mol. Biol.12:619-632 and Christensen et al. (1992) Plant Mol. Biol. 18:675-689);pEMU (Last et al. (1991) Theor. Appl. Genet. 81:581-588); MAS (Velten etal. (1984) EMBO J. 3:2723-2730); ALS promoter (U.S. Pat. No. 5,659,026),and the like. Other constitutive promoters include, for example, U.S.Pat. Nos. 5,608,149; 5,608,144; 5,604,121; 5,569,597; 5,466,785;5,399,680; 5,268,463; 5,608,142; and 6,177,611.

Tissue-preferred promoters can be utilized to target enhanced HPPDexpression within a particular plant tissue. Tissue-preferred promotersinclude those described in Yamamoto et al. (1997) Plant J.12(2):255-265; Kawamata et al. (1997) Plant Cell Physiol. 38(7):792-803;Hansen et al. (1997) Mol. Gen Genet. 254(3):337-343; Russell et al.(1997) Transgenic Res. 6(2):157-168; Rinehart et al. (1996) PlantPhysiol. 112(3):1331-1341; Van Camp et al. (1996) Plant Physiol.112(2):525-535; Canevascini et al. (1996) Plant Physiol. 112(2):513-524;Yamamoto et al. (1994) Plant Cell Physiol. 35(5):773-778; Lam (1994)Results Probl. Cell Differ. 20:181-196; Orozco et al. (1993) Plant MolBiol. 23(6):1129-1138; Matsuoka et al. (1993) Proc Natl. Acad. Sci. USA90(20):9586-9590; and Guevara-Garcia et al. (1993) Plant J.4(3):495-505. Such promoters can be modified, if necessary, for weakexpression.

Leaf-preferred promoters are known in the art. See, for example,Yamamoto et al. (1997) Plant J. 12(2):255-265; Kwon et al. (1994) PlantPhysiol. 105:357-67; Yamamoto et al. (1994) Plant Cell Physiol.35(5):773-778; Gotor et al. (1993) Plant J. 3:509-18; Orozco et al.(1993) Plant Mol. Biol. 23(6): 1129-1138; and Matsuoka et al. (1993)Proc. Natl. Acad. Sci. USA 90(20):9586-9590.

As discussed in more detail elsewhere herein, promoters that directexpression in a plastid, such as a chloroplast, can also be used toexpress the HPPD sequences or biologically active variants and fragmentsthereof.

Synthetic promoters can be used to express HPPD sequences orbiologically active variants and fragments thereof. In one non-limitingembodiment, the HPPD sequences are expressed with a syntheticconstitutive promoter (see for example U.S. Pat. Nos. 6,072,050 and6,555,673) or with a promoter disclosed in International Publication No.WO 2012/021794 and U.S. Pat. No. 8,993,837, entitled “Chimeric Promotersand Methods of Use.”), In still further embodiments, the HPPD variantsoperably linked to such synthetic promoters further comprise anArabidopsis ubiquitin3 gene terminator (Callis et al. (1995) Genetics139 (2), 921-939; Genbank L05363).

The expression cassette can also comprise a selectable marker gene forthe selection of transformed cells. Selectable marker genes are utilizedfor the selection of transformed cells or tissues. Marker genes includegenes encoding antibiotic resistance, such as those encoding neomycinphosphotransferase II (NEO) and hygromycin phosphotransferase (HPT), aswell as genes conferring resistance to herbicidal compounds, such asglyphosate, glufosinate ammonium, bromoxynil, sulfonylureas, dicamba,and 2,4-dichlorophenoxyacetate (2,4-D). Additional selectable markersinclude phenotypic markers such as β-galactosidase and fluorescentproteins such as green fluorescent protein (GFP) (Su et al. (2004)Biotechnol Bioeng 85:610-9 and Fetter et al. (2004) Plant Cell16:215-28), cyan florescent protein (CYP) (Bolte et al. (2004) J. CellScience 117:943-54 and Kato et al. (2002) Plant Physiol 129:913-42), andyellow florescent protein (PhiYFP™ from Evrogen, see, Bolte et al.(2004) J. Cell Science 117:943-54). For additional selectable markers,see generally, Yarranton (1992) Curr. Opin. Biotech. 3:506-511;Christopherson et al. (1992) Proc. Natl. Acad. Sci. USA 89:6314-6318;Yao et al. (1992) Cell 71:63-72; Reznikoff (1992) Mol. Microbiol.6:2419-2422; Barkley et al. (1980) in The Operon, pp. 177-220; Hu et al.(1987) Cell 48:555-566; Brown et al. (1987) Cell 49:603-612; Figge etal. (1988) Cell 52:713-722; Deuschle et al. (1989) Proc. Natl. Acad.Aci. USA 86:5400-5404; Fuerst et al. (1989) Proc. Natl. Acad. Sci. USA86:2549-2553; Deuschle et al. (1990) Science 248:480-483; Gossen (1993)Ph.D. Thesis, University of Heidelberg; Reines et al. (1993) Proc. Natl.Acad. Sci. USA 90:1917-1921; Labow et al. (1990) Mol. Cell. Biol.10:3343-3356; Zambretti et al. (1992) Proc. Natl. Acad. Sci. USA89:3952-3956; Baim et al. (1991) Proc. Natl. Acad. Sci. USA88:5072-5076; Wyborski et al. (1991) Nucleic Acids Res. 19:4647-4653;Hillenand-Wissman (1989) Topics Mol. Struc. Biol. 10:143-162; Degenkolbet al. (1991) Antimicrob. Agents Chemother. 35:1591-1595; Kleinschnidtet al. (1988) Biochemistry 27:1094-1104; Bonin (1993) Ph.D. Thesis,University of Heidelberg; Gossen et al. (1992) Proc. Natl. Acad. Sci.USA 89:5547-5551; Oliva et al. (1992) Antimicrob. Agents Chemother.36:913-919; Hlavka et al. (1985) Handbook of Experimental Pharmacology,Vol. 78 (Springer-Verlag, Berlin); Gill et al. (1988) Nature334:721-724. Such disclosures are herein incorporated by reference. Theabove list of selectable marker genes is not meant to be limiting. Anyselectable marker gene can be used in the present disclosure, includingfor example, DsRed as described in Example 1.

G. Stacking Other Traits of Interest

In some embodiments, the HPPD polynucleotides or active variants andfragments thereof disclosed herein are engineered into a molecularstack. Thus, the various plants, plant cells, plant parts, explants,seeds, and grain disclosed herein can further comprise one or moretraits of interest, and in more specific embodiments, the plant, plantpart or plant cell is stacked with any combination of polynucleotidesequences of interest in order to create plants with a desiredcombination of traits. As used herein, the term “stacked” includeshaving the multiple traits present in the same plant (i.e., both traitsare incorporated into the nuclear genome, one trait is incorporated intothe nuclear genome and one trait is incorporated into the genome of aplastid, or both traits are incorporated into the genome of a plastid).In one non-limiting example, “stacked traits” comprise a molecular stackwhere the sequences are physically adjacent to each other. A trait, asused herein, refers to the phenotype derived from a particular sequenceor groups of sequences. In one embodiment, the molecular stack comprisesat least one additional polynucleotide that also confers tolerance to atleast one HPPD inhibitor and/or at least one additional polynucleotidethat confers tolerance to a second herbicide.

Thus, in one embodiment, the plants, plant cells, plant parts, explants,seeds, and grain having the HPPD polynucleotide or active variants orfragments thereof disclosed herein is stacked with at least one otherHPPD sequence, include the HPPD sequence, and variants and fragmentthereof disclosed herein, as well as other HPPD sequence, which includebut are not limited to the HPPD sequences set forth in U.S. Pat. Nos.6,245,968 B1; 6,268,549; and 6,069,115; and international publication WO99/23886, each of which is herein incorporated by reference.

In still other embodiments, plants, plant cells, plant parts, explants,seeds, and grain comprise expression cassettes comprising the HPPDsequences or active variant and fragment thereof are stacked with asequence that confers tolerance to HPPD inhibitors through a differentmechanism than the HPPD polypeptide. For example, a P450 sequence couldbe employed which provides tolerance to HPPD-inhibitors by metabolism ofthe herbicide. Such sequences including, but are not limited to, theNSF1 gene. See, US 2007/0214515 and US 2008/0052797 both of which areherein incorporated by reference in their entirety.

In some embodiments, plants, plant cells, plant parts, explants, seeds,and grain having the HPPD polynucleotides or active variants or fragmentthereof may be stacked with other herbicide-tolerance traits to create atransgenic plant of the disclosure with further improved properties.Other herbicide-tolerance polynucleotides that could be used in suchembodiments include those conferring tolerance to glyphosate such as,for example, glyphosate N-acetyltransferase. See, for example,WO02/36782, US Publication 2004/0082770 and WO 2005/012515, U.S. Pat.Nos. 7,462,481, 7,405,074, each of which is herein incorporated byreference.

Additional glyphosate-tolerance traits include a sequence that encodes aglyphosate oxido-reductase enzyme as described more fully in U.S. Pat.Nos. 5,776,760 and 5,463,175. Other traits that could be combined withthe HPPD sequence disclosed herein include those derived frompolynucleotides that confer on the plant the capacity to produce ahigher level or glyphosate insensitive5-enolpyruvylshikimate-3-phosphate synthase (EPSPS), for example, asmore fully described in U.S. Pat. Nos. 6,248,876 B1; 5,627,061;5,804,425; 5,633,435; 5,145,783; 4,971,908; 5,312,910; 5,188,642;4,940,835; 5,866,775; 6,225,114 B1; 6,130,366; 5,310,667; 4,535,060;4,769,061; 5,633,448; 5,510,471; Re. 36,449; RE 37,287 E; and 5,491,288;and international publications WO 97/04103; WO 00/66746; WO 01/66704;and WO 00/66747. Other traits that could be combined with the HPPDsequences disclosed herein include those conferring tolerance tosulfonylurea and/or imidazolinone, for example, as described more fullyin U.S. Pat. Nos. 5,605,011; 5,013,659; 5,141,870; 5,767,361; 5,731,180;5,304,732; 4,761,373; 5,331,107; 5,928,937; and 5,378,824; andinternational publication WO 96/33270.

Additional known genes that confer tolerance to herbicides and can beemployed in the methods and compositions disclosed herein include, forexample e.g., auxin, HPPD, glyphosate, dicamba, glufosinate,sulfonylurea, bromoxynil and norflurazon herbicides can be stackedeither as a molecular stack or a breeding stack with plants expressingthe traits disclosed herein. Polynucleotide molecules encoding proteinsinvolved in herbicide tolerance include, but are not limited to, apolynucleotide molecule encoding 5-enolpyruvylshikimate-3-phosphatesynthase (EPSPS) disclosed in U.S. Pat. Nos. US39,247; 6,566,587 forimparting glyphosate tolerance; polynucleotide molecules encoding aglyphosate oxidoreductase (GOX) disclosed in U.S. Pat. No. 5,463,175 anda glyphosate-N-acetyl transferase (GAT) disclosed in U.S. Pat. Nos.7,622,641; 7,462,481; 7,531,339; 7,527,955; 7,709,709; 7,714,188 and7,666,643 also for providing glyphosate tolerance; dicamba monooxygenasedisclosed in U.S. Pat. No. 7,022,896 and WO2007146706A2 for providingdicamba tolerance; a polynucleotide molecule encoding AAD12 disclosed inU.S. Pat. App. Pub. No. 2005731044 or WO2007053482A2 or encoding AAD1disclosed in US20110124503A1 or U.S. Pat. No. 7,838,733 for providingtolerance to auxin herbicides (2,4-D); a polynucleotide moleculeencoding hydroxyphenylpyruvate dioxygenase (HPPD) for providingtolerance to HPPD inhibitors (e.g., hydroxyphenylpyruvate dioxygenase)disclosed in e.g., U.S. Pat. No. 7,935,869; US20090055976A1; andUS20110023180A1; each publication is herein incorporated by reference inits entirety.

In other embodiments, plants, plant cells, plant parts, explants, seeds,and grain having the HPPD sequence or an active variant or fragmentthereof is stacked with, for example, a sequence which confers toleranceto an acetolactate synthase (“ALS”) inhibitor. As used herein, an “ALSinhibitor-tolerant polypeptide” comprises any polypeptide which whenexpressed in a plant confers tolerance to at least one ALS inhibitor. Avariety of ALS inhibitors are known and include, for example,sulfonylurea, imidazolinone, triazolopyrimidines,pryimidinyoxy(thio)benzoates, and/or sulfonylaminocarbonyltriazolinoneherbicides. Additional ALS inhibitors are known and are disclosedelsewhere herein. It is known in the art that ALS mutations fall intodifferent classes with regard to tolerance to sulfonylureas,imidazolinones, triazolopyrimidines, and pyrimidinyl(thio)benzoates,including mutations having the following characteristics: (1) broadtolerance to all four of these groups; (2) tolerance to imidazolinonesand pyrimidinyl(thio)benzoates; (3) tolerance to sulfonylureas andtriazolopyrimidines; and (4) tolerance to sulfonylureas andimidazolinones.

Various ALS inhibitor-tolerant polypeptides can be employed. In someembodiments, the ALS inhibitor-tolerant polynucleotides contain at leastone nucleotide mutation resulting in one amino acid change in the ALSpolypeptide. In specific embodiments, the change occurs in one of sevensubstantially conserved regions of acetolactate synthase. See, forexample, Hattori et al. (1995) Molecular Genetics and Genomes246:419-425; Lee et al. (1998) EMBO Journal 7:1241-1248; Mazur et al.(1989) Ann. Rev. Plant Phys. 40:441-470; and U.S. Pat. No. 5,605,011,each of which is incorporated by reference in their entirety. The ALSinhibitor-tolerant polypeptide can be encoded by, for example, the SuRAor SuRB locus of ALS. In specific embodiments, the ALSinhibitor-tolerant polypeptide comprises the C3 ALS mutant, the HRA ALSmutant, the S4 mutant or the S4/HRA mutant or any combination thereof.Different mutations in ALS are known to confer tolerance to differentherbicides and groups (and/or subgroups) of herbicides; see, e.g.,Tranel and Wright (2002) Weed Science 50:700-712. See also, U.S. Pat.Nos. 5,605,011, 5,378,824, 5,141,870, and 5,013,659, each of which isherein incorporated by reference in their entirety. The soybean, maize,and Arabidopsis HRA sequences are disclosed, for example, inWO2007/024782, herein incorporated by reference.

In some embodiments, the ALS inhibitor-tolerant polypeptide conferstolerance to sulfonylurea and imidazolinone herbicides. The productionof sulfonylurea-tolerant plants and imidazolinone-tolerant plants isdescribed more fully in U.S. Pat. Nos. 5,605,011; 5,013,659; 5,141,870;5,767,361; 5,731,180; 5,304,732; 4,761,373; 5,331,107; 5,928,937; and5,378,824; and international publication WO 96/33270, which areincorporated herein by reference in their entireties for all purposes.In specific embodiments, the ALS inhibitor-tolerant polypeptidecomprises a sulfonamide-tolerant acetolactate synthase (otherwise knownas a sulfonamide-tolerant acetohydroxy acid synthase) or animidazolinone-tolerant acetolactate synthase (otherwise known as animidazolinone-tolerant acetohydroxy acid synthase).

In further embodiments, plants, plant cells, plant parts, explants,seeds, and grain having the HPPD sequence or an active variant orfragment thereof is stacked with, or example, a sequence which conferstolerance to an ALS inhibitor and glyphosate tolerance. In oneembodiment, the HPPD sequence or active variant or fragment thereof isstacked with HRA and a glyphosate N-acetyltransferase. See,WO2007/024782, 2008/0051288 and WO 2008/112019, each of which is hereinincorporated by reference.

In still other embodiments, plants, plant cells, plant parts, explants,seeds, and grain having the HPPD sequence or an active variant orfragment thereof may be stacked with, for example, aryloxyalkanoatedioxygenase polynucleotides (which confer tolerance to 2,4-D and otherphenoxy auxin herbicides as well as to aryloxyphenoxypropionateherbicides as described, for example, in WO2005/107437) anddicamba-tolerance polynucleotides as described, for example, in Hermanet al. (2005) J. Biol. Chem. 280: 24759-24767, auxin polypeptides and anacetyl coenzyme A carboxylase (ACCase) polypeptides.

Other examples of herbicide-tolerance traits that could be combined withthe plant or plant cell or plant part having the HPPD sequence or anactive variant or fragment thereof include those conferred bypolynucleotides encoding an exogenous phosphinothricinacetyltransferase, as described in U.S. Pat. Nos. 5,969,213; 5,489,520;5,550,318; 5,874,265; 5,919,675; 5,561,236; 5,648,477; 5,646,024;6,177,616; and 5,879,903. Plants containing an exogenousphosphinothricin acetyltransferase can exhibit improved tolerance toglufosinate herbicides, which inhibit the enzyme glutamine synthase.Other examples of herbicide-tolerance traits that could be combined withthe plants or plant cell or plant part having the HPPD sequence or anactive variant or fragment thereof include those conferred bypolynucleotides conferring altered protoporphyrinogen oxidase (protox)activity, as described in U.S. Pat. Nos. 6,288,306 B1; 6,282,837 B1; and5,767,373; and international publication WO 01/12825. Plants containingsuch polynucleotides can exhibit improved tolerance to any of a varietyof herbicides which target the protox enzyme (also referred to as“protox inhibitors”).

Other examples of herbicide-tolerance traits that could be combined withthe plants or plant cell or plant part having the HPPD sequence or anactive variant or fragment thereof include those conferring tolerance toat least one herbicide in a plant such as, for example, a maize plant orhorseweed. Herbicide-tolerant weeds are known in the art, as are plantsthat vary in their tolerance to particular herbicides. See, e.g., Greenand Williams (2004) “Correlation of Corn (Zea mays) Inbred Response toNicosulfuron and Mesotrione,” poster presented at the WSSA AnnualMeeting in Kansas City, Mo., Feb. 9-12, 2004; Green (1998) WeedTechnology 12: 474-477; Green and Ulrich (1993) Weed Science 41:508-516. The trait(s) responsible for these tolerances can be combinedby breeding or via other methods with the plants or plant cell or plantpart having the HPPD sequence or an active variant or fragment thereofto provide a plant of the disclosure as well as methods of use thereof.

In still further embodiments, the HPPD sequences can be stacked with atleast one polynucleotide encoding a homogentisate solanesyltransferase(HST). See, for example, WO2010023911 herein incorporated by referencein its entirety. In such embodiments, classes of herbicidalcompounds—which act wholly or in part by inhibiting HST can be appliedover the plants having the HTS polypeptide.

Plants, plant cells, plant parts, explants, seeds, and grain having theHPPD sequence or an active variant or fragment thereof can also becombined with at least one other trait to produce plants that furthercomprise a variety of desired trait combinations including, but notlimited to, traits desirable for animal feed such as high oil content(e.g., U.S. Pat. No. 6,232,529); balanced amino acid content (e.g.,hordothionins (U.S. Pat. Nos. 5,990,389; 5,885,801; 5,885,802; and5,703,409; 5,850,016); barley high lysine (Williamson et al. (1987) Eur.J. Biochem. 165: 99-106; and WO 98/20122) and high methionine proteins(Pedersen et al. (1986) J. Biol. Chem. 261: 6279; Kirihara et al. (1988)Gene 71: 359; and Musumura et al. (1989) Plant Mol. Biol. 12:123));increased digestibility (e.g., modified storage proteins (U.S.application Ser. No. 10/053,410, filed Nov. 7, 2001); and thioredoxins(U.S. application Ser. No. 10/005,429, filed Dec. 3, 2001)); thedisclosures of which are herein incorporated by reference. Desired traitcombinations also include LLNC (low linolenic acid content; see, e.g.,Dyer et al. (2002) Appl. Microbiol. Biotechnol. 59: 224-230) and OLCH(high oleic acid content; see, e.g., Fernandez-Moya et al. (2005) J.Agric. Food Chem. 53: 5326-5330).

Plants, plant cells, plant parts, explants, seeds, and grain having theHPPD sequence or an active variant or fragment thereof can also becombined with other desirable traits such as, for example, fumonisimdetoxification genes (U.S. Pat. No. 5,792,931), avirulence and diseaseresistance genes (Jones et al. (1994) Science 266: 789; Martin et al.(1993) Science 262: 1432; Mindrinos et al. (1994) Cell 78: 1089), andtraits desirable for processing or process products such as modifiedoils (e.g., fatty acid desaturase genes (U.S. Pat. No. 5,952,544; WO94/11516)); modified starches (e.g., ADPG pyrophosphorylases (AGPase),starch synthases (SS), starch branching enzymes (SBE), and starchdebranching enzymes (SDBE)); and polymers or bioplastics (e.g., U.S.Pat. No. 5,602,321; beta-ketothiolase, polyhydroxybutyrate synthase, andacetoacetyl-CoA reductase (Schubert et al. (1988) J. Bacteriol.170:5837-5847) facilitate expression of polyhydroxyalkanoates (PHAs));the disclosures of which are herein incorporated by reference. One couldalso combine herbicide-tolerant polynucleotides with polynucleotidesproviding agronomic traits such as male sterility (e.g., see U.S. Pat.No. 5,583,210), stalk strength, flowering time, or transformationtechnology traits such as cell cycle regulation or gene targeting (e.g.,WO 99/61619, WO 00/17364, and WO 99/25821); the disclosures of which areherein incorporated by reference.

In other embodiments, plants, plant cells, plant parts, explants, seeds,and grain having the HPPD sequence or an active variant or fragmentthereof may be stacked with any other polynucleotides encodingpolypeptides having pesticidal and/or insecticidal activity, such asBacillus thuringiensis toxic proteins (described in U.S. Pat. Nos.5,366,892; 5,747,450; 5,737,514; 5,723,756; 5,593,881; Geiser et al.(1986) Gene 48: 109; Lee et al. (2003) Appl. Environ. Microbiol. 69:4648-4657 (Vip3A); Galitzky et al. (2001) Acta Crystallogr. D. Biol.Crystallogr. 57: 1101-1109 (Cry3Bbl); and Herman et al. (2004) J. Agric.Food Chem. 52: 2726-2734 (CrylF)), lectins (Van Damme et al. (1994)Plant Mol. Biol. 24: 825, pentin (described in U.S. Pat. No. 5,981,722),and the like. The combinations generated can also include multiplecopies of any one of the polynucleotides of interest.

These stacked combinations can be created by any method including, butnot limited to, breeding plants by any conventional methodology, orgenetic transformation. If the sequences are stacked by geneticallytransforming the plants, the polynucleotide sequences of interest can becombined at any time and in any order. The traits can be introducedsimultaneously in a co-transformation protocol with the polynucleotidesof interest provided by any combination of transformation cassettes. Forexample, if two sequences will be introduced, the two sequences can becontained in separate transformation cassettes (trans) or contained onthe same transformation cassette (cis). Expression of the sequences canbe driven by the same promoter or by different promoters. In certaincases, it may be desirable to introduce a transformation cassette thatwill suppress the expression of the polynucleotide of interest. This maybe combined with any combination of other suppression cassettes oroverexpression cassettes to generate the desired combination of traitsin the plant. It is further recognized that polynucleotide sequences canbe stacked at a desired genomic location using a site-specificrecombination system. See, for example, WO99/25821, WO99/25854,WO99/25840, WO99/25855, and WO99/25853, all of which are hereinincorporated by reference.

H. Method of Introducing

Various methods can be used to introduce a sequence of interest into aplant or plant part. “Introducing” is intended to mean presenting to theplant, plant cell or plant part the polynucleotide or polypeptide insuch a manner that the sequence gains access to the interior of a cellof the plant. The methods of the disclosure do not depend on aparticular method for introducing a sequence into a plant or plant part,only that the polynucleotide or polypeptides gains access to theinterior of at least one cell of the plant. Methods for introducingpolynucleotide or polypeptides into plants are known in the artincluding, but not limited to, stable transformation methods, transienttransformation methods, and virus-mediated methods.

“Stable transformation” is intended to mean that the nucleotideconstruct introduced into a plant integrates into the genome of theplant and is capable of being inherited by the progeny thereof.“Transient transformation” is intended to mean that a polynucleotide isintroduced into the plant and does not integrate into the genome of theplant or a polypeptide is introduced into a plant.

Transformation protocols as well as protocols for introducingpolypeptides or polynucleotide sequences into plants may vary dependingon the type of plant or plant cell, i.e., monocot or dicot, targeted fortransformation. Suitable methods of introducing polypeptides andpolynucleotides into plant cells include microinjection (Crossway et al.(1986) Biotechniques 4:320-334), electroporation (Riggs et al. (1986)Proc. Natl. Acad. Sci. USA 83:5602-5606, Agrobacterium-mediatedtransformation (U.S. Pat. Nos. 5,563,055 and 5,981,840), direct genetransfer (Paszkowski et al. (1984) EMBO J 3:2717-2722), and ballisticparticle acceleration (see, for example, U.S. Pat. Nos. 4,945,050;5,879,918; 5,886,244; and, 5,932,782; Tomes et al. (1995) in Plant Cell,Tissue, and Organ Culture: Fundamental Methods, ed. Gamborg and Phillips(Springer-Verlag, Berlin); McCabe et al. (1988) Biotechnology6:923-926); and Lec1 transformation (WO 00/28058). Also see Weissingeret al. (1988) Ann. Rev. Genet. 22:421-477; Sanford et al. (1987)Particulate Science and Technology 5:27-37 (onion); Christou et al.(1988) Plant Physiol. 87:671-674 (soybean); McCabe et al. (1988)Bio/Technology 6:923-926 (soybean); Finer and McMullen (1991) In VitroCell Dev. Biol. 27P:175-182 (soybean); Singh et al. (1998) Theor. Appl.Genet. 96:319-324 (soybean); Datta et al. (1990) Biotechnology 8:736-740(rice); Klein et al. (1988) Proc. Natl. Acad. Sci. USA 85:4305-4309(maize); Klein et al. (1988) Biotechnology 6:559-563 (maize); U.S. Pat.Nos. 5,240,855; 5,322,783; and, 5,324,646; Klein et al. (1988) PlantPhysiol. 91:440-444 (maize); Fromm et al. (1990) Biotechnology 8:833-839(maize); Hooykaas-Van Slogteren et al. (1984) Nature (London)311:763-764; U.S. Pat. No. 5,736,369 (cereals); Bytebier et al. (1987)Proc. Natl. Acad. Sci. USA 84:5345-5349 (Liliaceae); De Wet et al.(1985) in The Experimental Manipulation of Ovule Tissues, ed. Chapman etal. (Longman, N.Y.), pp. 197-209 (pollen); Kaeppler et al. (1990) PlantCell Reports 9:415-418 and Kaeppler et al. (1992) Theor. Appl. Genet.84:560-566 (whisker-mediated transformation); D'Halluin et al. (1992)Plant Cell 4:1495-1505 (electroporation); Li et al. (1993) Plant CellReports 12:250-255 and Christou and Ford (1995) Annals of Botany75:407-413 (rice); Osjoda et al. (1996) Nature Biotechnology 14:745-750(maize via Agrobacterium tumefaciens); all of which are hereinincorporated by reference.

In specific embodiments, the HPPD sequences or active variant orfragments thereof can be provided to a plant, plant cell, plant part, orhost cell using a variety of transient transformation methods. Suchtransient transformation methods include, but are not limited to, theintroduction of the HPPD protein or active variants and fragmentsthereof directly into the plant, plant part, or plant cell. Such methodsinclude, for example, microinjection or particle bombardment. See, forexample, Crossway et al. (1986) Mol Gen. Genet. 202:179-185; Nomura etal. (1986) Plant Sci. 44:53-58; Hepler et al. (1994) Proc. Natl. Acad.Sci. 91: 2176-2180 and Hush et al. (1994) The Journal of Cell Science107:775-784, all of which are herein incorporated by reference.

In other embodiments, polynucleotides encoding the peptides of thedisclosure can be introduced into plants, plant parts, or plant cells bycontacting plants, plant parts, or plant cells with a virus or viralnucleic acids. Generally, such methods involve incorporating anucleotide construct of the disclosure within a DNA or RNA molecule. Itis recognized that the an HPPD sequence may be initially synthesized aspart of a viral polyprotein, which later may be processed by proteolysisin vivo or in vitro to produce the desired recombinant protein. Further,it is recognized that promoters of the disclosure also encompasspromoters utilized for transcription by viral RNA polymerases. Methodsfor introducing polynucleotides into plants and expressing a proteinencoded therein, involving viral DNA or RNA molecules, are known in theart. See, for example, U.S. Pat. Nos. 5,889,191, 5,889,190, 5,866,785,5,589,367, 5,316,931, and Porta et al. (1996) Molecular Biotechnology5:209-221; herein incorporated by reference.

Methods are known in the art for the targeted insertion of apolynucleotide at a specific location in the plant genome. In oneembodiment, the insertion of the polynucleotide at a desired genomiclocation is achieved using a site-specific recombination system. See,for example, WO99/25821, WO99/25854, WO99/25840, WO99/25855, andWO99/25853, all of which are herein incorporated by reference. Briefly,polynucleotides encoding polypeptides of the disclosure can be containedin transfer cassette flanked by two non-recombinogenic recombinationsites. The transfer cassette is introduced into a plant having stablyincorporated into its genome a target site which is flanked by twonon-recombinogenic recombination sites that correspond to the sites ofthe transfer cassette. An appropriate recombinase is provided and thetransfer cassette is integrated at the target site. The polynucleotideof interest is thereby integrated at a specific chromosomal position inthe plant genome. Other methods to target polynucleotides are set forthin WO 2009/114321 (herein incorporated by reference), which describes“custom” meganucleases produced to modify plant genomes, in particularthe genome of maize. See, also, Gao et al. (2010) Plant Journal1:176-187.

The plant cells that have been transformed may be grown into plants inaccordance with conventional ways. See, for example, McCormick et al.(1986) Plant Cell Reports 5:81-84. These plants may then be grown, andeither pollinated with the same transformed strain or different strains,and the resulting progeny having constitutive expression of the desiredphenotypic characteristic identified. Two or more generations may begrown to ensure that expression of the desired phenotypic characteristicis stably maintained and inherited and then seeds harvested to ensureexpression of the desired phenotypic characteristic has been achieved.In this manner, the present disclosure provides transformed seeds (alsoreferred to as “transgenic seed”) having a polynucleotide encodingpolypeptides of the disclosure, for example, an expression cassette ofthe disclosure, stably incorporated into their genome.

I. Chloroplast Transformation

In specific embodiments, the HPPD polypeptides and active variants andfragments thereof, and polynucleotide encoding the same, do not compriseor encode a CTP. Such polynucleotides can be expressed from the nucleargenome of plants, plant cells, plant parts, explants, seeds, and grainand the polypeptides acting from the cytoplasm still conferinsensitivity of the cell, plant or plant cell to an HPPD inhibitor. Instill other embodiments, the HPPD polynucleotides lacking thechloroplast transit peptide are introduced directly into the chloroplastvia chloroplast transformation. Such methods of chloroplasttransformation are discussed in detail elsewhere herein. Thus,chloroplasts having stably incorporated in their genome a polynucleotideencoding an HPPD polypeptide or an active variant or fragment thereoflacking a CTP as described herein are provided.

In other embodiments, only the HPPD polypeptides or active variants andfragments thereof are in the chloroplast of a plant or plant cell. Insuch instances, the HPPD polypeptide can comprise a chloroplast transitpeptide and can be expressed from a polynucleotide incorporated into thenuclear genome. In such an instance, the HPPD polypeptide is transportedinto the chloroplast, the CTP is removed, and the mature form of theHPPD polypeptide is then found within the chloroplast.

In other embodiments, the polynucleotide encoding the HPPD polypeptideor active variant or fragment thereof is incorporated directly into thegenome of the chloroplast. In such instances, the HPPD polypeptide neednot comprise a CTP.

The sequences to be targeted to the chloroplast may be optimized forexpression in the chloroplast to account for differences in codon usagebetween the plant nucleus and this organelle. In this manner, thepolynucleotide of interest may be synthesized usingchloroplast-preferred codons. See, for example, U.S. Pat. No. 5,380,831,herein incorporated by reference.

As used herein, a “plastid” refers to an organelle present in plantcells that stores and manufactures chemical compounds used by the cell,such as starch, fatty acids, terpenes, and that has been derived from aproplastid. Thus, plastids of plants typically have the same geneticcontent. Plastids include chloroplasts, which are responsible forphotosynthesis, amyloplasts, chromoplasts, statoliths, leucoplasts,elaioplasts, and proteinoplasts.

The plastid genome is circular and varies in size among plant speciesfrom about 120 to about 217 kilobase pairs (kb). The genome typicallyincludes a large inverted repeat, which can contain up to about 76kilobase pairs, but which is more typically in the range of about 20 toabout 30 kilobase pairs. The inverted repeat present in the plastidgenome of various organisms has been described (Palmer (1990) TrendsGenet 6:115-120).

Methods are known in the art for introducing genes into the plastidgenome. See, for example, Svab et al. (1990) Proc. Natl. Acad. Sci. USA87: 8526-8530; Svab and Maliga (1993) Proc. Natl. Acad. Sci. USA 90:913-917; Svab and Maliga (1993) EMBO J. 12: 601-606; and U.S. Pat. Nos.5,451,513 and 5,545,818; each of which is herein incorporated byreference in its entirety.

One method involves the integration of a polynucleotide of interest intothe plastid genome through homologous recombination. Such methodsinvolve the introduction of a polynucleotide of interest flanked byregions of homology with regions of the plastid genome into a plantcell. Delivery of the polynucleotide of interest into the plant cell canbe via any method of transformation known in the art, including thosedescribed elsewhere herein. These include, but are not limited to,particle gun delivery (Svab, Z. et al. (1990) Proc Natl Acad Sci USA87:8526-8530; Svab and Maliga (1993) Proc Natl Acad Sci USA 90:913-917;and Staub and Maliga (1993) EMBO J 12:601-606; and U.S. Pat. Nos.5,451,513 and 5,545,818; each of which is herein incorporated byreference in its entirety). In some species, protoplasts can also beused for chloroplast transformation (O'Neill et al. (1993) Plant J3:729-38; and Spoerlein et al. (1991) Theor Appl Gen 82:717-722; each ofwhich is herein incorporated by reference in its entirety). Once thepolynucleotide of interest flanked by the homologous regions enters thecell, the polynucleotide of interest will be integrated within theplastid genome.

The homologous regions flanking the polynucleotide of interest, and insome embodiments, its operably linked promoter, and in particularembodiments, the selectable marker gene as well may vary in length. Insome embodiments, the region of homology with the plastid genome isabout 50, 75, 100, 200, 300, 400, 500, 600, 700, 800, 900, 1000 basepairs or greater in length. In most instances, the frequency ofrecombination and thus the frequency of obtaining plants havingtransformed plastids decreases with the decreasing size of thehomologous regions. In those embodiments wherein the regions of homologyare present in the inverted repeat regions of the plastid genome, twocopies of the polynucleotide of interest are expected per transformedplastid.

In some embodiments, the polynucleotide of interest can be co-deliveredwith a selectable marker gene that is active in the plastid. Theselectable marker gene and the polynucleotide of interest can be presenton a single DNA construct or on separate constructs. A number of markershave been developed for use with plant cells, such as resistance tochloramphenicol, the aminoglycoside G418, hygromycin, or the like. Genesconferring resistance to kanamycin (NPTII or AphA6) have been used as aselectable marker for plastid transformation (Carrer et al. (1993) MolGen Genetics 241:49-56; and Huang et al. (2002) Mol Gen Genomics268:19-27; each of which is herein incorporated by reference in itsentirety). Other genes which encode a product involved in chloroplastmetabolism may also be used as selectable markers.

Another example of a selectable marker gene for plastid transformationis a selectable marker gene that confers resistance to a substance whichinhibits protein synthesis by the plastids, such that cells which haveacquired the phenotype are selected for by contacting the cells with asubstance which inhibits protein synthesis by the plastids. The plastidDNA encoding the nonlethal selectable phenotype may comprise 16Sribosomal DNA mutated to confer resistance to the effects ofstreptomycin, or to spectinomycin, or to both antibioticssimultaneously. Expression of heterologous genes that modify non-lethalantibiotics such as streptomycin or spectinomycin by phosphorylation,adenylation or acetylation also are suitable for the selection ofplastid transformation events. Another non-limiting example of a genethat confers resistance to streptomycin and spectinomycin is thebacterial aadA gene that codes for streptomycin/spectinomycinadenyltransferase (Svab et al. (1993) Proc Natl Acad Sci USA90:913-917). The aadA gene product allows for continued growth andgreening of cells in the presence of streptomycin or spectinomycin whosechloroplasts comprise the selectable marker gene product. Cells which donot contain the selectable marker gene product are bleached. Selectionfor the aadA gene marker is thus based on identification of plant cellswhich are not bleached by the presence of streptomycin or spectinomycin,in the plant growth medium.

Other examples of selectable marker genes are those that conferresistance to an herbicide, including a photosystem II herbicide, suchas a triazine herbicide, specifically the triazine herbicide atrazine.This phenotype not only provides nonlethal selection, but also providesherbicide resistance. Genes that provide resistance to plant herbicidessuch as glyphosate, bromoxynil, or imidazolinone may find use as aselectable marker gene. Such genes have been reported (Stalker et al.(1985) J Biol Chem 260:4724-4728 (glyphosate resistant EPSP); Stalker eta. (1985) J Biol Chem 263:6310-6314 (bromoxynil resistant nitrilasegene); and Sathasivan et al. (1990) Nucl Acids Res 18:2188 (AHASimidazolinone resistance gene); each of which is herein incorporated byreference in its entirety).

The selectable marker gene and/or the polynucleotide of interest can beplaced under the regulatory control of a chloroplast 5′ promoter and 3′transcription termination regions, such as the tobacco 16S rRNA promoterrrn region and rps16 3′ termination region. Numerous additional promoterregions may also be used to drive expression of the selectable markergene and/or the polynucleotide of interest, including various plastidpromoters and bacterial promoters which have been shown to function inplant plastids. Further, if nuclear expression of the selectable markergene and/or the polynucleotide of interest is not desired, plastidintrons can be incorporated into the selectable marker gene and/or thepolynucleotide of interest. Certain classes of plastid introns cannot becorrectly spliced out in the nucleus, thereby preventing expression ofthe selectable marker gene and/or the polynucleotide of interest withinthe nucleus. The polynucleotide of interest and/or the heterologouspolynucleotide encoding the cell proliferation factor may be optimizedfor expression in the chloroplast to account for differences in codonusage between the plant nucleus and this organelle. In this manner, thepolynucleotide may be synthesized using chloroplast-preferred codons.See, for example, U.S. Pat. No. 5,380,831, herein incorporated byreference.

An additional method of plastid transformation occurs through thetransactivation of a silent plastid-borne transgene by tissue-preferredexpression of a nuclear-encoded and plastid-directed RNA polymerase.Such a system has been reported in McBride et al. (1994) Proc. Natl.Acad. Sci. USA 91: 7301-7305, which is herein incorporated by referencein its entirety. In these methods, the heterologous polynucleotideencoding the cell proliferation factor is introduced into the cell andexpressed prior to, during, or immediately after the expression of theplastid-directed RNA polymerase.

In order to select those cells having transformed plastids, followingintroduction of the chloroplast transformation vectors, the treatedtissue is placed on tissue culture medium containing the appropriateselection agent. After a suitable period of incubation on selectionmedium, transformed cells can be identified and grown to a stage thatallows regeneration of the whole plants. The regeneration processes arebasically identical to those used for standard nuclear transformationevents. Special care must be taken to ensure that selection andregeneration conditions promote the elimination of most wild-typechloroplast genomes. The status of the proportion of wild-type totransformed chloroplast genomes can be monitored by standard moleculartechniques including Southern and PCR analysis.

For tobacco and a number of other species, leaves are a preferred targetfor plastid transformation. Chloroplast transformation has beendescribed for tobacco (Svab, Zora; Hajdukiewicz et al. (1990)Proceedings of the National Academy of Sciences of the United States ofAmerica 87(21):8526-30), Arabidopsis (Sikdar, S. R.; Serino, G.;Chaudhuri, S.; Maliga, P (1998) Plant Cell Reports 18(1-2):20-24),tomato (Ruf et al. (2001) Nature Biotechnology: 19(9):870-875), potato(Sidorov et al. (1999) Plant Journal 19(2): 209-216). For soybean,embryogenic suspension cultures can be targeted for transformation(Dufourmantel et al. (2004) Plant Molecular Biology: 55(4), 479-489;US20070039075 A1).

II. Methods of Use

A. Methods for Increasing Concentration of at Least One HPPD Sequence oran Active Variant or Fragment Therefore in a Plant or Plant Part

A method for increasing the concentration of an HPPD polypeptidedisclosed herein or an active variant or fragment thereof in plants,plant cells, plant parts, explants, seeds, grain or a chloroplast isprovided. HPPD activity and insensitivity to HPPD inhibitors arediscussed in detail elsewhere herein. In further embodiments, theconcentration/level of the HPPD polypeptide is increased in a plant orplant part by at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%,100%, 200%, 500%, 1000%, 5000%, or 10,000% relative to an appropriatecontrol plant, plant part, or cell which did not have the HPPD sequence.In still other embodiments, the level of the HPPD polypeptide in theplant or plant part is increased by 10, 20, 30, 40, 50, 60, 70, 80, 90,100 fold or more compared to the level of the native HPPD sequence. Suchan increase in the level of the HPPD polypeptide can be achieved in avariety of ways including, for example, by the expression of multiplecopies of one or more HPPD polypeptide and/or by employing a promoter todrive higher levels of expression of the sequence.

In specific embodiments, the polypeptide or the HPPD polynucleotide oractive variant or fragment thereof is introduced into plants, plantcells, plant parts, explants, seeds, and grain. Subsequently, a plantcell having the introduced sequence of the disclosure is selected usingmethods known to those of skill in the art such as, but not limited to,Southern blot analysis, DNA sequencing, PCR analysis, or phenotypicanalysis. A plant cell altered or modified by the foregoing embodimentsis grown under plant forming conditions for a time sufficient tomodulate the concentration and/or activity of polypeptides of thepresent disclosure in the plant. Plant forming conditions are well knownin the art and discussed briefly elsewhere herein.

In one embodiment, a method of producing an HPPD herbicide tolerantplant cell is provided and comprises transforming a plant cell with apolynucleotide encoding an HPPD polypeptide or active variant orfragment thereof. In specific embodiments, the method further comprisesselecting a plant cell which is resistant or tolerant to an HPPDherbicide by growing the plant cells in a sufficient concentration of anHPPD herbicide, such that the herbicide bleaches the plant cells whichdo not comprise the HPPD polypeptide of interest.

It is recognized that the incubation of the cells with the HPPDherbicide can occur before or after transformation with the HPPDpolynucleotide of interest. For example, in one embodiment, a methodcomprises culturing a plant cell in the presence of a sufficientconcentration of an HPPD herbicide such that said plant cell displaysbleaching and then transforming into the bleached plant cells apolynucleotide encoding an HPPD polypeptide as disclosed herein. Theplant cells are then grown, wherein the transformed plants cells nolonger display bleaching. See, for example, U.S. Pat. No. 6,791,014,herein incorporated by reference it its entirety.

It is also recognized that the level and/or activity of the native HPPDsequence in a plant may be altered by employing a polynucleotide that isnot capable of directing, in a transformed plant, the expression of aprotein or an RNA. For example, the HPPD polynucleotide or activevariant or fragment thereof disclosed herein may be used to designpolynucleotide constructs that can be employed in methods for alteringor mutating a genomic nucleotide sequence in an organism. Suchpolynucleotide constructs include, but are not limited to, RNA:DNAvectors, RNA:DNA mutational vectors, RNA:DNA repair vectors,mixed-duplex oligonucleotides, self-complementary RNA:DNAoligonucleotides, and recombinogenic oligonucleobases. Such nucleotideconstructs and methods of use are known in the art. See, U.S. Pat. Nos.5,565,350; 5,731,181; 5,756,325; 5,760,012; 5,795,972; and 5,871,984;all of which are herein incorporated by reference. See also, WO98/49350, WO 99/07865, WO 99/25821, and Beetham et al. (1999) Proc.Natl. Acad. Sci. USA 96:8774-8778; herein incorporated by reference.

It is therefore recognized that methods of the present disclosure do notdepend on the incorporation of the entire polynucleotide into thegenome, only that the plant or cell thereof is altered as a result ofthe introduction of the polynucleotide into a cell. In one embodiment ofthe disclosure, the genome may be altered following the introduction ofthe polynucleotide into a cell. Alterations to the genome of the presentdisclosure include, but are not limited to, additions, deletions, andsubstitutions of nucleotides into the genome. While the methods of thepresent disclosure do not depend on additions, deletions, andsubstitutions of any particular number of nucleotides, it is recognizedthat such additions, deletions, or substitutions comprises at least onenucleotide.

B. Method of Producing Crops and Controlling Weeds

Methods for controlling weeds in an area of cultivation, preventing thedevelopment or the appearance of herbicide resistant weeds in an area ofcultivation, producing a crop, and increasing crop safety are provided.The term “controlling,” and derivations thereof, for example, as in“controlling weeds” refers to one or more of inhibiting the growth,germination, reproduction, and/or proliferation of; and/or killing,removing, destroying, or otherwise diminishing the occurrence and/oractivity of a weed.

As used herein, an “area of cultivation” comprises any region in whichone desires to grow a plant. Such areas of cultivations include, but arenot limited to, a field in which a plant is cultivated (such as a cropfield, a sod field, a tree field, a managed forest, a field forculturing fruits and vegetables, etc), a greenhouse, a growth chamber,etc.

As used herein, by “selectively controlled” it is intended that themajority of weeds in an area of cultivation are significantly damaged orkilled, while if crop plants are also present in the field, the majorityof the crop plants are not significantly damaged. Thus, a method isconsidered to selectively control weeds when at least 55%, 60%, 65%,70%, 75%, 80%, 85%, 90%, 95%, or more of the weeds are significantlydamaged or killed, while if crop plants are also present in the field,less than 45%, 40%, 35%, 30%, 25%, 20%, 15%, 10%, 5%, or 1% of the cropplants are significantly damaged or killed.

Methods provided comprise planting the an area of cultivation with atransgenic seed derived there from a plant having an HPPD sequence oractive variant or fragment thereof disclosed herein or, and in specificembodiments, applying to the crop, seed, weed or area of cultivationthereof an effective amount of a herbicide of interest. It is recognizedthat the herbicide can be applied before or after the crop is planted inthe area of cultivation (e.g., seeds are planted). Herbicideapplications can include an application of an HPPD inhibitor including,but not limited to, triketones (such as, mesotrione, sulcotrione,topremezone, and tembotrione) including agriculturally suitable salts(e.g., sodium salts) thereof; isoxazoles (such as, pyrasulfotole andisoxaflutole) including agriculturally suitable salts (e.g., sodiumsalts) thereof; pyrazoles (such as, benzofenap, pyrazoxyfen, andpyrazolynate) including agriculturally suitable salts (e.g., sodiumsalts) thereof; and benzobicyclon, including agriculturally suitablesalts (e.g., sodium salts) thereof. See, WO2005/053407. In specificembodiments, a combination of two or more HPPD inhibitors is applied.Generally, the effective amount of herbicide applied to the field issufficient to selectively control the weeds without significantlyaffecting the crop.

“Weed” as used herein refers to a plant which is not desirable in aparticular area. Conversely, a “crop plant” as used herein refers to aplant which is desired in a particular area, such as, for example, amaize or soy plant. Thus, in some embodiments, a weed is a non-cropplant or a non-crop species, while in some embodiments, a weed is a cropspecies which is sought to be eliminated from a particular area, suchas, for example, an inferior and/or non-transgenic soy plant in a fieldplanted with a plant having the HPPD sequence disclosed herein or anactive variant or fragment thereof.

Further provided is a method for producing a crop by growing a cropplant that is tolerant to an HPPD herbicide as a result of beingtransformed with an HPPD polynucleotide or active variant or fragmentthereof disclosed herein, under conditions such that the crop plantproduces a crop, and harvesting the crop. Preferably, an HPPD inhibitoris applied to the plant, or in the vicinity of the plant, at aconcentration effective to control weeds without preventing thetransgenic crop plant from growing and producing the crop. Theapplication of the HPPD inhibitor can be before planting, or at any timeafter planting up to and including the time of harvest. The HPPDinhibitor can be applied once or multiple times. The timing of the HPPDinhibitor application, amount applied, mode of application, and otherparameters will vary based upon the specific nature of the crop plantand the growing environment, and can be readily determined by one ofskill in the art. The disclosure further provides the crop produced bythis method.

Further provided are methods for the propagation of a plant containing aHPPD polypeptide or active variant or fragment thereof. The plant canbe, for example, a monocot or a dicot. In one aspect, propagationentails crossing a plant containing a HPPD polynucleotide transgene witha second plant, such that at least some progeny of the cross displayHPPD inhibitor tolerance.

The methods of the disclosure further allow for the development ofherbicide applications to be used with the plants having the HPPDsequence or active variants or fragments thereof. In such methods, theenvironmental conditions in an area of cultivation are evaluated.Environmental conditions that can be evaluated include, but are notlimited to, ground and surface water pollution concerns, intended use ofthe crop, crop tolerance, soil residuals, weeds present in area ofcultivation, soil texture, pH of soil, amount of organic matter in soil,application equipment, and tillage practices. Upon the evaluation of theenvironmental conditions, an effective amount of a combination ofherbicides can be applied to the crop, crop part, seed of the crop orarea of cultivation.

Any herbicide or combination of herbicides can be applied to the planthaving the HPPD sequence or active variant or fragment thereof disclosedherein or transgenic seed derived there from, crop part, or the area ofcultivation containing the crop plant. By “treated with a combinationof” or “applying a combination of” herbicides to a crop, area ofcultivation or field” it is intended that a particular field, crop orweed is treated with each of the herbicides and/or chemicals indicatedto be part of the combination so that a desired effect is achieved,i.e., so that weeds are selectively controlled while the crop is notsignificantly damaged. The application of each herbicide and/or chemicalmay be simultaneous or the applications may be at different times(sequential), so long as the desired effect is achieved. Furthermore,the application can occur prior to the planting of the crop.

Classifications of herbicides (i.e., the grouping of herbicides intoclasses and subclasses) are well-known in the art and includeclassifications by HRAC (Herbicide Resistance Action Committee) and WSSA(the Weed Science Society of America) (see also, Retzinger andMallory-Smith (1997) Weed Technology 11: 384-393). An abbreviatedversion of the HRAC classification (with notes regarding thecorresponding WSSA group) is set forth below in Table 1.

Herbicides can be classified by their mode of action and/or site ofaction and can also be classified by the time at which they are applied(e.g., preemergent or postemergent), by the method of application (e.g.,foliar application or soil application), or by how they are taken up byor affect the plant or by their structure. “Mode of action” generallyrefers to the metabolic or physiological process within the plant thatthe herbicide inhibits or otherwise impairs, whereas “site of action”generally refers to the physical location or biochemical site within theplant where the herbicide acts or directly interacts. Herbicides can beclassified in various ways, including by mode of action and/or site ofaction (see, e.g., Table 1 which shows an abbreviated version of HRACHerbicide Classification).

Often, a herbicide-tolerance gene that confers tolerance to a particularherbicide or other chemical on a plant expressing it will also confertolerance to other herbicides or chemicals in the same class orsubclass, for example, a class or subclass set forth in Table 1. Thus,in some embodiments, a transgenic plant is tolerant to more than oneherbicide or chemical in the same class or subclass, such as, forexample, an HPPD inhibitor, glyphosate, an ALS chemistry, an inhibitorof PPO, a sulfonylurea, and/or a synthetic auxin.

Typically, the plants of the present disclosure can tolerate treatmentwith different types of herbicides (i.e., herbicides having differentmodes of action and/or different sites of action) thereby permittingimproved weed management strategies that are recommended in order toreduce the incidence and prevalence of herbicide-tolerant weeds.

TABLE 1 I. ALS Inhibitors (WSSA Group 2) A. Sulfonylureas 1.Azimsulfuron 2. Chlorimuron-ethyl 3. Metsulfuron-methyl 4. Nicosulfuron5. Rimsulfuron 6. Sulfometuron-methyl 7. Thifensulfuron-methyl 8.Tribenuron-methyl 9. Amidosulfuron 10. Bensulfuron-methyl 11.Chlorsulfuron 12. Cinosulfuron 13. Cyclosulfamuron 14.Ethametsulfuron-methyl 15. Ethoxysulfuron 16. Flazasulfuron 17.Flupyrsulfuron-methyl 18. Foramsulfuron 19. Imazosulfuron 20.Iodosulfuron-methyl 21. Mesosulfuron-methyl 22. Oxasulfuron 23.Primisulfuron-methyl 24. Prosulfuron 25. Pyrazosulfuron-ethyl 26.Sulfosulfuron 27. Triasulfuron 28. Trifloxysulfuron 29.Triflusulfuron-methyl 30. Tritosulfuron 31. Halosulfuron-methyl 32.Flucetosulfuron B. Sulfonylaminocarbonyltriazolinones 1. Flucarbazone 2.Procarbazone C. Triazolopyrimidines 1. Cloransulam-methyl 2. Flumetsulam3. Diclosulam 4. Florasulam 5. Metosulam 6. Penoxsulam 7. Pyroxsulam D.Pyrimidinyloxy(thio)benzoates 1. Bispyribac 2. Pyriftalid 3.Pyribenzoxim 4. Pyrithiobac 5. Pyriminobac-methyl E. Imidazolinones 1.Imazapyr 2. Imazethapyr 3. Imazaquin 4. Imazapic 5.Imazamethabenz-methyl 6. Imazamox II. Other Herbicides--ActiveIngredients/Additional Modes of Action A. Inhibitors of Acetyl CoAcarboxylase (ACCase) (WSSA Group 1) 1. Aryloxyphenoxypropionates(‘FOPs’) a. Quizalofop-P-ethyl b. Diclofop-methyl c.Clodinafop-propargyl d. Fenoxaprop-P-ethyl e. Fluazifop-P-butyl f.Propaquizafop g. Haloxyfop-P-methyl h. Cyhalofop-butyl i.Quizalofop-P-ethyl 2. Cyclohexanediones (‘DIMs’) a. Alloxydim b.Butroxydim c. Clethodim d. Cycloxydim e. Sethoxydim f. Tepraloxydim g.Tralkoxydim B. Inhibitors of Photosystem II- HRAC Group C1/WSSA Group5 1. Triazines a. Ametryne b. Atrazine c. Cyanazine d. Desmetryne e.Dimethametryne f. Prometon g. Prometryne h. Propazine i. Simazine j.Simetryne k. Terbumeton l. Terbuthylazine m. Terbutryne n. Trietazine 2.Triazinones a. Hexazinone b. Metribuzin c. Metamitron 3. Triazolinone a.Amicarbazone 4. Uracils a. Bromacil b. Lenacil c. Terbacil 5.Pyridazinones a. Pyrazon 6. Phenyl carbamates a. Desmedipham b.Phenmedipham C. Inhibitors of Photosystem II-- HRAC Group C2/WSSA Group7 1. Ureas a. Fluometuron b. Linuron c. Chlorobromuron d. Chlorotolurone. Chloroxuron f. Dimefuron g. Diuron h. Ethidimuron i. Fenuron j.Isoproturon k. Isouron l. Methabenzthiazuron m. Metobromuron n.Metoxuron o. Monolinuron p. Neburon q. Siduron r. Tebuthiuron 2. Amidesa. Propanil b. Pentanochlor D. Inhibitors of Photosystem II-- HRAC GroupC3/WSSA Group 6 1. Nitriles a. Bromofenoxim b. Bromoxynil c. Ioxynil 2.Benzothiadiazinone (Bentazon) a. Bentazon 3. Phenylpyridazines a.Pyridate b. Pyridafol E. Photosystem-I-electron diversion(Bipyridyliums) (WSSA Group 22) 1. Diquat 2. Paraquat F. Inhibitors ofPPO (protoporphyrinogen oxidase) (WSSA Group 14) 1. Diphenylethers a.Acifluorfen-Na b. Bifenox c. Chlomethoxyfen d. Fluoroglycofen-ethyl e.Fomesafen f. Halosafen g. Lactofen h. Oxyfluorfen 2. Phenylpyrazoles a.Fluazolate b. Pyraflufen-ethyl 3. N-phenylphthalimides a. Cinidon-ethylb. Flumioxazin c. Flumiclorac-pentyl 4. Thiadiazoles a.Fluthiacet-methyl b. Thidiazimin 5. Oxadiazoles a. Oxadiazon b.Oxadiargyl 6. Triazolinones a. Carfentrazone-ethyl b. Sulfentrazone 7.Oxazolidinediones a. Pentoxazone 8. Pyrimidindiones a. Benzfendizone b.Butafenicil 9. Others a. Pyrazogyl b. Profluazol G. Bleaching:Inhibition of carotenoid biosynthesis at the phytoene desaturase step(PDS) (WSSA Group 12) 1. Pyridazinones a. Norflurazon 2.Pyridinecarboxamides a. Diflufenican b. Picolinafen 3. Others a.Beflubutamid b. Fluridone c. Flurochloridone d. Flurtamone H. Bleaching:Inhibition of 4- hydroxyphenyl-pyruvate-dioxygenase (4-HPPD) (WSSA Group28) 1. Triketones a. Mesotrione b. Sulcotrione c. topramezone d.tembotrione 2. Isoxazoles a. Pyrasulfotole b. Isoxaflutole 3. Pyrazolesa. Benzofenap b. Pyrazoxyfen c. Pyrazolynate 4. Others a. BenzobicyclonI. Bleaching: Inhibition of carotenoid biosynthesis (unknown target)(WSSA Group 11 and 13) 1. Triazoles (WSSA Group 11) a. Amitrole 2.Isoxazolidinones (WSSA Group 13) a. Clomazone 3. Ureas a. Fluometuron 3.Diphenylether a. Aclonifen J. Inhibition of EPSP Synthase 1. Glycines(WSSA Group 9) a. Glyphosate b. Sulfosate K. Inhibition of glutaminesynthetase 1. Phosphinic Acids a. Glufosinate-ammonium b. Bialaphos L.Inhibition of DHP (dihydropteroate) synthase (WSSA Group 18) 1 Carbamates a. Asulam M. Microtubule Assembly Inhibition (WSSA Group3) 1. Dinitroanilines a. Benfluralin b. Butralin c. Dinitramine d.Ethalfluralin e. Oryzalin f. Pendimethalin g. Trifluralin 2.Phosphoroamidates a. Amiprophos-methyl b. Butamiphos 3. Pyridines a.Dithiopyr b. Thiazopyr 4. Benzamides a. Pronamide b. Tebutam 5.Benzenedicarboxylic acids a. Chlorthal-dimethyl N. Inhibition ofmitosis/microtubule organization WSSA Group 23) 1. Carbamates a.Chlorpropham b. Propham c. Carbetamide O. Inhibition of cell division(Inhibition of very long chain fatty acids as proposed mechanism; WSSAGroup 15) 1. Chloroacetamides a. Acetochlor b. Alachlor c. Butachlor d.Dimethachlor e. Dimethanamid f. Metazachlor g. Metolachlor h. Pethoxamidi. Pretilachlor j. Propachlor k. Propisochlor l. Thenylchlor 2.Acetamides a. Diphenamid b. Napropamide c. Naproanilide 3. Oxyacetamidesa. Flufenacet b. Mefenacet 4. Tetrazolinones a. Fentrazamide 5. Othersa. Anilofos b. Cafenstrole c. Indanofan d. Piperophos P. Inhibition ofcell wall (cellulose) synthesis 1. Nitriles (WSSA Group 20) a.Dichlobenil b. Chlorthiamid 2. Benzamides (isoxaben (WSSA Group 21)) a.Isoxaben 3. Triazolocarboxamides (flupoxam) a. Flupoxam Q. Uncoupling(membrane disruption): (WSSA Group 24) 1. Dinitrophenols a. DNOC b.Dinoseb c. Dinoterb R. Inhibition of Lipid Synthesis by other than ACCinhibition 1. Thiocarbamates (WSSA Group 8) a. Butylate b. Cycloate c.Dimepiperate d. EPTC e. Esprocarb f. Molinate g. Orbencarb h. Pebulatei. Prosulfocarb j. Benthiocarb k. Tiocarbazil l. Triallate m. Vernolate2. Phosphorodithioates a. Bensulide 3. Benzofurans a. Benfuresate b.Ethofumesate 4. Halogenated alkanoic acids (WSSA Group 26) a. TCA b.Dalapon c. Flupropanate S. Synthetic auxins (IAA-like) (WSSA Group 4) 1.Phenoxycarboxylic acids a. Clomeprop b. 2,4-D c. Mecoprop 2. Benzoicacids a. Dicamba b. Chloramben c. TBA 3. Pyridine carboxylic acids a.Clopyralid b. Fluroxypyr c. Picloram d. Tricyclopyr 4. Quinolinecarboxylic acids a. Quinclorac b. Quinmerac 5. Others (benazolin-ethyl)a. Benazolin-ethyl T. Inhibition of Auxin Transport 1. Phthalamates;semicarbazones (WSSA Group 19) a. Naptalam b. Diflufenzopyr-Na U. OtherMechanism of Action 1. Arylaminopropionic acids a. Flamprop-M-methyl/-isopropyl 2. Pyrazolium a. Difenzoquat 3. Organoarsenicals a. DSMA b.MSMA 4. Others a. Bromobutide b. Cinmethylin c. Cumyluron d. Dazomet e.Daimuron-methyl f. Dimuron g. Etobenzanid h. Fosamine i. Metam j.Oxaziclomefone k. Oleic acid l. Pelargonic acid m. Pyributicarb

In still further methods, an HPPD inhibitor can be applied alone or incombination with another herbicide of interest and can be applied to theplants having the HPPD sequence as disclosed herein or their area ofcultivation.

Additional herbicide treatment that can be applied over the plant orseeds having the HPPD polypeptides or active variants and fragmentsthereof include, but are not limited to: acetochlor, acifluorfen and itssodium salt, aclonifen, acrolein (2-propenal), alachlor, alloxydim,ametryn, amicarbazone, amidosulfuron, aminopyralid, amitrole, ammoniumsulfamate, anilofos, asulam, atrazine, azimsulfuron, beflubutamid,benazolin, benazolin-ethyl, bencarbazone, benfluralin, benfuresate,bensulfuron-methyl, bensulide, bentazone, benzobicyclon, benzofenap,bifenox, bilanafos, bispyribac and its sodium salt, bromacil,bromobutide, bromofenoxim, bromoxynil, bromoxynil octanoate, butachlor,butafenacil, butamifos, butralin, butroxydim, butylate, cafenstrole,carbetamide, carfentrazone-ethyl, catechin, chlomethoxyfen, chloramben,chlorbromuron, chlorflurenol-methyl, chloridazon, chlorimuron-ethyl,chlorotoluron, chlorpropham, chlorsulfuron, chlorthal-dimethyl,chlorthiamid, cinidon-ethyl, cinmethylin, cinosulfuron, clethodim,clodinafop-propargyl, clomazone, clomeprop, clopyralid,clopyralid-olamine, cloransulam-methyl, CUH-35 (2-methoxyethyl2-[[[4-chloro-2-fluoro-5-[(1-methyl-2-propynyl)oxy]phenyl](3-fluorobenzoyl)-amino]carbonyl]-1-cyclohexene-1-carboxylate),cumyluron, cyanazine, cycloate, cyclosulfamuron, cycloxydim,cyhalofop-butyl, 2,4-D and its butotyl, butyl, isoctyl and isopropylesters and its dimethylammonium, diolamine and trolamine salts,daimuron, dalapon, dalapon-sodium, dazomet, 2,4-DB and itsdimethylammonium, potassium and sodium salts, desmedipham, desmetryn,dicamba and its diglycolammonium, dimethylammonium, potassium and sodiumsalts, dichlobenil, dichlorprop, diclofop-methyl, diclosulam,difenzoquat metilsulfate, diflufenican, diflufenzopyr, dimefuron,dimepiperate, dimethachlor, dimethametryn, dimethenamid, dimethenamid-P,dimethipin, dimethylarsinic acid and its sodium salt, dinitramine,dinoterb, diphenamid, diquat dibromide, dithiopyr, diuron, DNOC,endothal, EPTC, esprocarb, ethalfluralin, ethametsulfuron-methyl,ethofumesate, ethoxyfen, ethoxysulfuron, etobenzanid, fenoxaprop-ethyl,fenoxaprop-P-ethyl, fentrazamide, fenuron, fenuron-TCA, flamprop-methyl,flamprop-M-isopropyl, flamprop-M-methyl, flazasulfuron, florasulam,fluazifop-butyl, fluazifop-P-butyl, flucarbazone, flucetosulfuron,fluchloralin, flufenacet, flufenpyr, flufenpyr-ethyl, flumetsulam,flumiclorac-pentyl, flumioxazin, fluometuron, fluoroglycofen-ethyl,flupyrsulfuron-methyl and its sodium salt, flurenol, flurenol-butyl,fluridone, flurochloridone, fluroxypyr, flurtamone, fluthiacet-methyl,fomesafen, foramsulfuron, fosamine-ammonium, glufosinate,glufosinate-ammonium, glyphosate and its salts such as ammonium,isopropylammonium, potassium, sodium (including sesquisodium) andtrimesium (alternatively named sulfosate) (See, WO2007/024782, hereinincorporated by reference), halosulfuron-methyl, haloxyfop-etotyl,haloxyfop-methyl, hexazinone, HOK-201(N-(2,4-difluorophenyl)-1,5-dihydro-N-(1-methylethyl)-5-oxo-1-[(tetrahydro-2H-pyran-2-yl)methyl]-4H-1,2,4-triazole-4-carboxamide),imazamethabenz-methyl, imazamox, imazapic, imazapyr, imazaquin,imazaquin-ammonium, imazethapyr, imazethapyr-ammonium, imazosulfuron,indanofan, iodosulfuron-methyl, ioxynil, ioxynil octanoate,ioxynil-sodium, isoproturon, isouron, isoxaben, isoxaflutole,pyrasulfotole, lactofen, lenacil, linuron, maleic hydrazide, MCPA andits salts (e.g., MCPA-dimethylammonium, MCPA-potassium and MCPA-sodium,esters (e.g., MCPA-2-ethylhexyl, MCPA-butotyl) and thioesters (e.g.,MCPA-thioethyl), MCPB and its salts (e.g., MCPB-sodium) and esters(e.g., MCPB-ethyl), mecoprop, mecoprop-P, mefenacet, mefluidide,mesosulfuron-methyl, mesotrione, metam-sodium, metamifop, metamitron,metazachlor, methabenzthiazuron, methylarsonic acid and its calcium,monoammonium, monosodium and disodium salts, methyldymron, metobenzuron,metobromuron, metolachlor, S-metholachlor, metosulam, metoxuron,metribuzin, metsulfuron-methyl, molinate, monolinuron, naproanilide,napropamide, naptalam, neburon, nicosulfuron, norflurazon, orbencarb,oryzalin, oxadiargyl, oxadiazon, oxasulfuron, oxaziclomefone,oxyfluorfen, paraquat dichloride, pebulate, pelargonic acid,pendimethalin, penoxsulam, pentanochlor, pentoxazone, perfluidone,pethoxyamid, phenmedipham, picloram, picloram-potassium, picolinafen,pinoxaden, piperofos, pretilachlor, primisulfuron-methyl, prodiamine,profoxydim, prometon, prometryn, propachlor, propanil, propaquizafop,propazine, propham, propisochlor, propoxycarbazone, propyzamide,prosulfocarb, prosulfuron, pyraclonil, pyraflufen-ethyl, pyrasulfotole,pyrazogyl, pyrazolynate, pyrazoxyfen, pyrazosulfuron-ethyl,pyribenzoxim, pyributicarb, pyridate, pyriftalid, pyriminobac-methyl,pyrimisulfan, pyrithiobac, pyrithiobac-sodium, pyroxsulam, quinclorac,quinmerac, quinoclamine, quizalofop-ethyl, quizalofop-P-ethyl,quizalofop-P-tefuryl, rimsulfuron, sethoxydim, siduron, simazine,simetryn, sulcotrione, sulfentrazone, sulfometuron-methyl,sulfosulfuron, 2,3,6-TBA, TCA, TCA-sodium, tebutam, tebuthiuron,tefuryltrione, tembotrione, tepraloxydim, terbacil, terbumeton,terbuthylazine, terbutryn, thenylchlor, thiazopyr, thiencarbazone,thifensulfuron-methyl, thiobencarb, tiocarbazil, topramezone,tralkoxydim, tri-allate, triasulfuron, triaziflam, tribenuron-methyl,triclopyr, triclopyr-butotyl, triclopyr-triethylammonium, tridiphane,trietazine, trifloxysulfuron, trifluralin, triflusulfuron-methyl,tritosulfuron and vernolate.

Additional herbicides include those that are applied over plants havinghomogentisate solanesyltransferase (HST) polypeptide such as thosedescribed in International Publication No. WO 2010/029311(A2), hereinincorporated by reference it its entirety.

Other suitable herbicides and agricultural chemicals are known in theart, such as, for example, those described in International PublicationNo. WO 2005/041654. Other herbicides also include bioherbicides such asthose produced by Streptomyces hygroscopicus, Alternaria destruensSimmons, Colletotrichum gloeosporiodes (Penz.) Penz. & Sacc., Drechsieramonoceras (MTB-951), Myrothecium verrucaria (Albertini & Schweinitz)Ditmar: Fries, Phytophthora palmivora (Butl.) Butl. and Pucciniathlaspeos Schub. Combinations of various herbicides can result in agreater-than-additive (i.e., synergistic) effect on weeds and/or aless-than-additive effect (i.e. safening) on crops or other desirableplants. In certain instances, combinations of HPPD herbicides with otherherbicides having a similar spectrum of control but a different mode ofaction will be particularly advantageous for preventing the developmentof resistant weeds.

The time at which a herbicide is applied to an area of interest (and anyplants therein) may be important in optimizing weed control. The time atwhich a herbicide is applied may be determined with reference to thesize of plants and/or the stage of growth and/or development of plantsin the area of interest, e.g., crop plants or weeds growing in the area.

Ranges of the effective amounts of herbicides can be found, for example,in various publications from University Extension services. See, forexample, Bernards et al. (2006) Guide for Weed Management in Nebraska(www.ianrpubs.url.edu/sendlt/ec130); Regher et al. (2005) Chemical WeedControl for Fields Crops, Pastures, Rangeland, and Noncropland, KansasState University Agricultural Extension Station and Corporate ExtensionService; Zollinger et al. (2006) North Dakota Weed Control Guide, NorthDakota Extension Service, and the Iowa State University Extension atwww.weeds.iastate.edu, each of which is herein incorporated byreference.

Many plant species can be controlled (i.e., killed or damaged) by theherbicides described herein. Accordingly, the methods of the disclosureare useful in controlling these plant species where they are undesirable(i.e., where they are weeds). These plant species include crop plants aswell as species commonly considered weeds, including but not limited tospecies such as: blackgrass (Alopecurus myosuroides), giant foxtail(Setaria faberi), large crabgrass (Digitaria sanguinalis), Surinam grass(Brachiaria decumbens), wild oat (Avena fatua), common cocklebur(Xanthium pensylvanicum), common lambsquarters (Chenopodium album),morning glory (Ipomoea coccinea), pigweed (Amaranthus spp.), velvetleaf(Abutilion theophrasti), common barnyardgrass (Echinochloa crus-galli),bermudagrass (Cynodon dactylon), downy brome (Bromus tectorum),goosegrass (Eleusine indica), green foxtail (Setaria viridis), Italianryegrass (Lolium multiflorum), Johnsongrass (Sorghum halepense), lessercanarygrass (Phalaris minor), windgrass (Apera spica-venti), woolycupgrass (Erichloa villosa), yellow nutsedge (Cyperus esculentus),common chickweed (Stellaria media), common ragweed (Ambrosiaartemisiifolia), Kochia scoparia, horseweed (Conyza canadensis), rigidryegrass (Lolium rigidum), goosegrass (Eleucine indica), hairy fleabane(Conyza bonariensis), buckhorn plantain (Plantago lanceolata), tropicalspiderwort (Commelina benghalensis), field bindweed (Convolvulusarvensis), purple nutsedge (Cyperus rotundus), redvine (Brunnichiaovata), hemp sesbania (Sesbania exaltata), sicklepod (Sennaobtusifolia), Texas blueweed (Helianthus ciliaris), and Devil's claws(Proboscidea louisianica). In other embodiments, the weed comprises aherbicide-resistant ryegrass, for example, a glyphosate resistantryegrass, a paraquat resistant ryegrass, a ACCase-inhibitor resistantryegrass, and a non-selective herbicide resistant ryegrass.

In some embodiments, a plant having the HPPD sequence disclosed hereinor active variants and fragments thereof is not significantly damaged bytreatment with an HPPD inhibitor applied to that plant, whereas anappropriate control plant is significantly damaged by the sametreatment.

Generally, an HPPD inhibitor is applied to a particular field (and anyplants growing in it) no more than 1, 2, 3, 4, 5, 6, 7, or 8 times ayear, or no more than 1, 2, 3, 4, or 5 times per growing season.

Thus, methods of the disclosure encompass applications of herbicidewhich are “preemergent,” “postemergent,” “preplant incorporation” and/orwhich involve seed treatment prior to planting.

In one embodiment, methods are provided for coating seeds. The methodscomprise coating a seed with an effective amount of a herbicide or acombination of herbicides (as disclosed elsewhere herein). The seeds canthen be planted in an area of cultivation. Further provided are seedshaving a coating comprising an effective amount of a herbicide or acombination of herbicides (as disclosed elsewhere herein). In otherembodiments, the seeds can be coated with at least one fungicide and/orat least one insecticide and/or at least one herbicide or anycombination thereof.

“Preemergent” refers to a herbicide which is applied to an area ofinterest (e.g., a field or area of cultivation) before a plant emergesvisibly from the soil. “Postemergent” refers to a herbicide which isapplied to an area after a plant emerges visibly from the soil. In someinstances, the terms “preemergent” and “postemergent” are used withreference to a weed in an area of interest, and in some instances theseterms are used with reference to a crop plant in an area of interest.When used with reference to a weed, these terms may apply to only aparticular type of weed or species of weed that is present or believedto be present in the area of interest. While any herbicide may beapplied in a preemergent and/or postemergent treatment, some herbicidesare known to be more effective in controlling a weed or weeds whenapplied either preemergence or postemergence. For example, rimsulfuronhas both preemergence and postemergence activity, while other herbicideshave predominately preemergence (metolachlor) or postemergence(glyphosate) activity. These properties of particular herbicides areknown in the art and are readily determined by one of skill in the art.Further, one of skill in the art would readily be able to selectappropriate herbicides and application times for use with the transgenicplants of the disclosure and/or on areas in which transgenic plants ofthe disclosure are to be planted. “Preplant incorporation” involves theincorporation of compounds into the soil prior to planting.

Thus, improved methods of growing a crop and/or controlling weeds suchas, for example, “pre-planting burn down,” are provided wherein an areais treated with herbicides prior to planting the crop of interest inorder to better control weeds. The disclosure also provides methods ofgrowing a crop and/or controlling weeds which are “no-till” or“low-till” (also referred to as “reduced tillage”). In such methods, thesoil is not cultivated or is cultivated less frequently during thegrowing cycle in comparison to traditional methods; these methods cansave costs that would otherwise be incurred due to additionalcultivation, including labor and fuel costs.

The term “safener” refers to a substance that when added to a herbicideformulation eliminates or reduces the phytotoxic effects of theherbicide to certain crops. One of ordinary skill in the art wouldappreciate that the choice of safener depends, in part, on the cropplant of interest and the particular herbicide or combination ofherbicides. Exemplary safeners suitable for use with the presentlydisclosed herbicide compositions include, but are not limited to, thosedisclosed in U.S. Pat. Nos. 4,808,208; 5,502,025; 6,124,240 and U.S.Patent Application Publication Nos. 2006/0148647; 2006/0030485;2005/0233904; 2005/0049145; 2004/0224849; 2004/0224848; 2004/0224844;2004/0157737; 2004/0018940; 2003/0171220; 2003/0130120; 2003/0078167,the disclosures of which are incorporated herein by reference in theirentirety. The methods of the disclosure can involve the use ofherbicides in combination with herbicide safeners such as benoxacor, BCS(1-bromo-4-[(chloromethyl) sulfonyl]benzene), cloquintocet-mexyl,cyometrinil, dichlormid, 2-(dichloromethyl)-2-methyl-1,3-dioxolane (MG191), fenchlorazole-ethyl, fenclorim, flurazole, fluxofenim, furilazole,isoxadifen-ethyl, mefenpyr-diethyl, methoxyphenone((4-methoxy-3-methylphenyl)(3-methylphenyl)-methanone), naphthalicanhydride (1,8-naphthalic anhydride) and oxabetrinil to increase cropsafety. Antidotally effective amounts of the herbicide safeners can beapplied at the same time as the compounds of this disclosure, or appliedas seed treatments. Therefore an aspect of the present disclosurerelates to the use of a mixture comprising an HPPD inhibitor, at leastone other herbicide, and an antidotally effective amount of a herbicidesafener.

Seed treatment is useful for selective weed control, because itphysically restricts antidoting to the crop plants. Therefore in oneembodiment, a method for selectively controlling the growth of weeds ina field comprising treating the seed from which the crop is grown withan antidotally effective amount of safener and treating the field withan effective amount of herbicide to control weeds.

An antidotally effective amount of a safener is present where a desiredplant is treated with the safener so that the effect of a herbicide onthe plant is decreased in comparison to the effect of the herbicide on aplant that was not treated with the safener; generally, an antidotallyeffective amount of safener prevents damage or severe damage to theplant treated with the safener. One of skill in the art is capable ofdetermining whether the use of a safener is appropriate and determiningthe dose at which a safener should be administered to a crop.

As used herein, an “adjuvant” is any material added to a spray solutionor formulation to modify the action of an agricultural chemical or thephysical properties of the spray solution. See, for example, Green andFoy (2003) “Adjuvants: Tools for Enhancing Herbicide Performance,” inWeed Biology and Management, ed. Inderjit (Kluwer Academic Publishers,The Netherlands). Adjuvants can be categorized or subclassified asactivators, acidifiers, buffers, additives, adherents, antiflocculants,antifoamers, defoamers, antifreezes, attractants, basic blends,chelating agents, cleaners, colorants or dyes, compatibility agents,cosolvents, couplers, crop oil concentrates, deposition agents,detergents, dispersants, drift control agents, emulsifiers, evaporationreducers, extenders, fertilizers, foam markers, formulants, inerts,humectants, methylated seed oils, high load COCs, polymers, modifiedvegetable oils, penetrators, repellants, petroleum oil concentrates,preservatives, rainfast agents, retention aids, solubilizers,surfactants, spreaders, stickers, spreader stickers, synergists,thickeners, translocation aids, uv protectants, vegetable oils, waterconditioners, and wetting agents.

In addition, methods of the disclosure can comprise the use of aherbicide or a mixture of herbicides, as well as, one or more otherinsecticides, fungicides, nematocides, bactericides, acaricides, growthregulators, chemosterilants, semiochemicals, repellents, attractants,pheromones, feeding stimulants or other biologically active compounds orentomopathogenic bacteria, virus, or fungi to form a multi-componentmixture giving an even broader spectrum of agricultural protection.Examples of such agricultural protectants which can be used in methodsof the disclosure include: insecticides such as abamectin, acephate,acetamiprid, amidoflumet (S-1955), avermectin, azadirachtin,azinphos-methyl, bifenthrin, bifenazate, buprofezin, carbofuran, cartap,chlorfenapyr, chlorfluazuron, chlorpyrifos, chlorpyrifos-methyl,chromafenozide, clothianidin, cyflumetofen, cyfluthrin, beta-cyfluthrin,cyhalothrin, lambda-cyhalothrin, cypermethrin, cyromazine, deltamethrin,diafenthiuron, diazinon, dieldrin, diflubenzuron, dimefluthrin,dimethoate, dinotefuran, diofenolan, emamectin, endosulfan,esfenvalerate, ethiprole, fenothiocarb, fenoxycarb, fenpropathrin,fenvalerate, fipronil, flonicamid, flubendiamide, flucythrinate,tau-fluvalinate, flufenerim (UR-50701), flufenoxuron, fonophos,halofenozide, hexaflumuron, hydramethylnon, imidacloprid, indoxacarb,isofenphos, lufenuron, malathion, metaflumizone, metaldehyde,methamidophos, methidathion, methomyl, methoprene, methoxychlor,metofluthrin, monocrotophos, methoxyfenozide, nitenpyram, nithiazine,novaluron, noviflumuron (XDE-007), oxamyl, parathion, parathion-methyl,permethrin, phorate, phosalone, phosmet, phosphamidon, pirimicarb,profenofos, profluthrin, pymetrozine, pyrafluprole, pyrethrin,pyridalyl, pyriprole, pyriproxyfen, rotenone, ryanodine, spinosad,spirodiclofen, spiromesifen (BSN 2060), spirotetramat, sulprofos,tebufenozide, teflubenzuron, tefluthrin, terbufos, tetrachlorvinphos,thiacloprid, thiamethoxam, thiodicarb, thiosultap-sodium, tralomethrin,triazamate, trichlorfon and triflumuron; fungicides such as acibenzolar,aldimorph, amisulbrom, azaconazole, azoxystrobin, benalaxyl, benomyl,benthiavalicarb, benthiavalicarb-isopropyl, binomial, biphenyl,bitertanol, blasticidin-S, Bordeaux mixture (Tribasic copper sulfate),boscalid/nicobifen, bromuconazole, bupirimate, buthiobate, carboxin,carpropamid, captafol, captan, carbendazim, chloroneb, chlorothalonil,chlozolinate, clotrimazole, copper oxychloride, copper salts such ascopper sulfate and copper hydroxide, cyazofamid, cyflunamid, cymoxanil,cyproconazole, cyprodinil, dichlofluanid, diclocymet, diclomezine,dicloran, diethofencarb, difenoconazole, dimethomorph, dimoxystrobin,diniconazole, diniconazole-M, dinocap, discostrobin, dithianon,dodemorph, dodine, econazole, etaconazole, edifenphos, epoxiconazole,ethaboxam, ethirimol, ethridiazole, famoxadone, fenamidone, fenarimol,fenbuconazole, fencaramid, fenfuram, fenhexamide, fenoxanil,fenpiclonil, fenpropidin, fenpropimorph, fentin acetate, fentinhydroxide, ferbam, ferfurazoate, ferimzone, fluazinam, fludioxonil,flumetover, fluopicolide, fluoxastrobin, fluquinconazole,fluquinconazole, flusilazole, flusulfamide, flutolanil, flutriafol,folpet, fosetyl-aluminum, fuberidazole, furalaxyl, furametapyr,hexaconazole, hymexazole, guazatine, imazalil, imibenconazole,iminoctadine, iodicarb, ipconazole, iprobenfos, iprodione, iprovalicarb,isoconazole, isoprothiolane, kasugamycin, kresoxim-methyl, mancozeb,mandipropamid, maneb, mapanipyrin, mefenoxam, mepronil, metalaxyl,metconazole, methasulfocarb, metiram, metominostrobin/fenominostrobin,mepanipyrim, metrafenone, miconazole, myclobutanil, neo-asozin (ferricmethanearsonate), nuarimol, octhilinone, ofurace, orysastrobin,oxadixyl, oxolinic acid, oxpoconazole, oxycarboxin, paclobutrazol,penconazole, pencycuron, penthiopyrad, perfurazoate, phosphonic acid,phthalide, picobenzamid, picoxystrobin, polyoxin, probenazole,prochloraz, procymidone, propamocarb, propamocarb-hydrochloride,propiconazole, propineb, proquinazid, prothioconazole, pyraclostrobin,pryazophos, pyrifenox, pyrimethanil, pyrifenox, pyrolnitrine,pyroquilon, quinconazole, quinoxyfen, quintozene, silthiofam,simeconazole, spiroxamine, streptomycin, sulfur, tebuconazole,techrazene, tecloftalam, tecnazene, tetraconazole, thiabendazole,thifluzamide, thiophanate, thiophanate-methyl, thiram, tiadinil,tolclofos-methyl, tolyfluanid, triadimefon, triadimenol, triarimol,triazoxide, tridemorph, trimoprhamide tricyclazole, trifloxystrobin,triforine, triticonazole, uniconazole, validamycin, vinclozolin, zineb,ziram, and zoxamide; nematocides such as aldicarb, oxamyl andfenamiphos; bactericides such as streptomycin; acaricides such asamitraz, chinomethionat, chlorobenzilate, cyhexatin, dicofol,dienochlor, etoxazole, fenazaquin, fenbutatin oxide, fenpropathrin,fenpyroximate, hexythiazox, propargite, pyridaben and tebufenpyrad; andbiological agents including entomopathogenic bacteria, such as Bacillusthuringiensis subsp. Aizawai, Bacillus thuringiensis subsp. Kurstaki,and the encapsulated delta-endotoxins of Bacillus thuringiensis (e.g.,Cellcap, MPV, MPVII); entomopathogenic fungi, such as green muscardinefungus; and entomopathogenic virus including baculovirus,nucleopolyhedro virus (NPV) such as HzNPV, AfNPV; and granulosis virus(GV) such as CpGV.

The methods of controlling weeds can further include the application ofa biologically effective amount of a herbicide of interest or a mixtureof herbicides, and an effective amount of at least one additionalbiologically active compound or agent and can further comprise at leastone of a surfactant, a solid diluent or a liquid diluent. Examples ofsuch biologically active compounds or agents are: insecticides such asabamectin, acephate, acetamiprid, amidoflumet (S-1955), avermectin,azadirachtin, azinphos-methyl, bifenthrin, binfenazate, buprofezin,carbofuran, chlorfenapyr, chlorfluazuron, chlorpyrifos,chlorpyrifos-methyl, chromafenozide, clothianidin, cyfluthrin,beta-cyfluthrin, cyhalothrin, lambda-cyhalothrin, cypermethrin,cyromazine, deltamethrin, diafenthiuron, diazinon, diflubenzuron,dimethoate, diofenolan, emamectin, endosulfan, esfenvalerate, ethiprole,fenothicarb, fenoxycarb, fenpropathrin, fenvalerate, fipronil,flonicamid, flucythrinate, tau-fluvalinate, flufenerim (UR-50701),flufenoxuron, fonophos, halofenozide, hexaflumuron, imidacloprid,indoxacarb, isofenphos, lufenuron, malathion, metaldehyde,methamidophos, methidathion, methomyl, methoprene, methoxychlor,monocrotophos, methoxyfenozide, nithiazin, novaluron, noviflumuron(XDE-007), oxamyl, parathion, parathion-methyl, permethrin, phorate,phosalone, phosmet, phosphamidon, pirimicarb, profenofos, pymetrozine,pyridalyl, pyriproxyfen, rotenone, spinosad, spiromesifin (BSN 2060),sulprofos, tebufenozide, teflubenzuron, tefluthrin, terbufos,tetrachlorvinphos, thiacloprid, thiamethoxam, thiodicarb,thiosultap-sodium, tralomethrin, trichlorfon and triflumuron; fungicidessuch as acibenzolar, azoxystrobin, benomyl, blasticidin-S, Bordeauxmixture (tribasic copper sulfate), bromuconazole, carpropamid, captafol,captan, carbendazim, chloroneb, chlorothalonil, copper oxychloride,copper salts, cyflufenamid, cymoxanil, cyproconazole, cyprodinil,(S)-3,5-dichloro-N-(3-chloro-1-ethyl-1-methyl-2-oxopropyl)-4-methylbenzamide(RH 7281), diclocymet (S-2900), diclomezine, dicloran, difenoconazole,(S)-3,5-dihydro-5-methyl-2-(methylthio)-5-phenyl-3-(phenyl-amino)-4H-imidazol-4-one(RP 407213), dimethomorph, dimoxystrobin, diniconazole, diniconazole-M,dodine, edifenphos, epoxiconazole, famoxadone, fenamidone, fenarimol,fenbuconazole, fencaramid (SZX0722), fenpiclonil, fenpropidin,fenpropimorph, fentin acetate, fentin hydroxide, fluazinam, fludioxonil,flumetover (RPA 403397), flumorf/flumorlin (SYP-L190), fluoxastrobin(HEC 5725), fluquinconazole, flusilazole, flutolanil, flutriafol,folpet, fosetyl-aluminum, furalaxyl, furametapyr (S-82658),hexaconazole, ipconazole, iprobenfos, iprodione, isoprothiolane,kasugamycin, kresoxim-methyl, mancozeb, maneb, mefenoxam, mepronil,metalaxyl, metconazole, metomino-strobin/fenominostrobin (SSF-126),metrafenone (AC375839), myclobutanil, neo-asozin (ferricmethane-arsonate), nicobifen (BAS 510), orysastrobin, oxadixyl,penconazole, pencycuron, probenazole, prochloraz, propamocarb,propiconazole, proquinazid (DPX-KQ926), prothioconazole (JAU 6476),pyrifenox, pyraclostrobin, pyrimethanil, pyroquilon, quinoxyfen,spiroxamine, sulfur, tebuconazole, tetraconazole, thiabendazole,thifluzamide, thiophanate-methyl, thiram, tiadinil, triadimefon,triadimenol, tricyclazole, trifloxystrobin, triticonazole, validamycinand vinclozolin; nematocides such as aldicarb, oxamyl and fenamiphos;bactericides such as streptomycin; acaricides such as amitraz,chinomethionat, chlorobenzilate, cyhexatin, dicofol, dienochlor,etoxazole, fenazaquin, fenbutatin oxide, fenpropathrin, fenpyroximate,hexythiazox, propargite, pyridaben and tebufenpyrad; and biologicalagents including entomopathogenic bacteria, such as Bacillusthuringiensis subsp. Aizawai, Bacillus thuringiensis subsp. Kurstaki,and the encapsulated delta-endotoxins of Bacillus thuringiensis (e.g.,Cellcap, MPV, MPVII); entomopathogenic fungi, such as green muscardinefungus; and entomopathogenic virus including baculovirus,nucleopolyhedro virus (NPV) such as HzNPV, AfNPV; and granulosis virus(GV) such as CpGV. Methods of the disclosure may also comprise the useof plants genetically transformed to express proteins (such as Bacillusthuringiensis delta-endotoxins) toxic to invertebrate pests. In suchembodiments, the effect of exogenously applied invertebrate pest controlcompounds may be synergistic with the expressed toxin proteins. Generalreferences for these agricultural protectants include The PesticideManual, 13th Edition, C. D. S. Tomlin, Ed., British Crop ProtectionCouncil, Farnham, Surrey, U. K., 2003 and The BioPesticide Manual,2^(nd) Edition, L. G. Copping, Ed., British Crop Protection Council,Farnham, Surrey, U. K., 2001.

In certain instances, combinations with other invertebrate pest controlcompounds or agents having a similar spectrum of control but a differentmode of action will be particularly advantageous for resistancemanagement. Thus, compositions of the present disclosure can furthercomprise a biologically effective amount of at least one additionalinvertebrate pest control compound or agent having a similar spectrum ofcontrol but a different mode of action. Contacting a plant geneticallymodified to express a plant protection compound (e.g., protein) or thelocus of the plant with a biologically effective amount of a compound ofthis disclosure can also provide a broader spectrum of plant protectionand be advantageous for resistance management.

Thus, methods of controlling weeds can employ a herbicide or herbicidecombination and may further comprise the use of insecticides and/orfungicides, and/or other agricultural chemicals such as fertilizers. Theuse of such combined treatments of the disclosure can broaden thespectrum of activity against additional weed species and suppress theproliferation of any resistant biotypes.

Methods can further comprise the use of plant growth regulators such asaviglycine, N-(phenylmethyl)-1H-purin-6-amine, ethephon, epocholeone,gibberellic acid, gibberellin A₄ and A₇, harpin protein, mepiquatchloride, prohexadione calcium, prohydrojasmon, sodium nitrophenolateand trinexapac-methyl, and plant growth modifying organisms such asBacillus cereus strain BP01.

C. Method of Detections

Methods for detecting an HPPD polypeptide or an active variant orfragment thereof are provided. Such methods comprise analyzing planttissues to detect such polypeptides or the polynucleotides encoding thesame. The detection methods can directly assay for the presence of theHPPD polypeptide or polynucleotide or the detection methods canindirectly assay for the sequences by assaying the phenotype of the cellplant, plant cell or plant explant expressing the sequence.

In one embodiment, the HPPD polypeptide is detected in the plant tissueusing an immunoassay comprising an antibody or antibodies thatspecifically recognizes an HPPD polypeptide or active variant orfragment thereof. In specific embodiments, the antibody or antibodieswhich are used are raised to an HPPD polypeptide or active variant orfragment thereof as disclosed herein.

By “specifically or selectively binds” is intended that the bindingagent has a binding affinity for a given HPPD polypeptide or fragment orvariant disclosed herein, which is greater than 10%, 9%, 8%, 7%, 6%, 5%,4%, 3%, 2% or 1% of the binding affinity for a known HPPD sequence. Oneof skill will be aware of the proper controls that are needed to carryout such a determination

By “antibodies that specifically bind” is intended that the antibodieswill not substantially cross react with another polypeptide. By “notsubstantially cross react” is intended that the antibody or fragmentthereof has a binding affinity for the other polypeptide which is lessthan 10%, less than 5%, or less than 1%, of the binding affinity for theHPPD polypeptide or active fragment or variant thereof.

In an aspect, the HPPD polypeptide can be detected in plant tissueextracts by subjecting the extract to trypsin digestion, followed byLC-MS. For example, tryptic fragments can be partially separated fromeach other by reverse-phase liquid chromatography and the columneffluent directed into a mass spectrometer. A specific peptide unique tothe transgenically expressed HPPD is detected by adjusting theinstrument setting so as to record and quantify the peptide according tothe exact mass of the signature peptide. Such an exemplary method isdescribed in Example 1 herein.

In still other embodiments, the HPPD polypeptide or active variant orfragment thereof can be inferred in a plant tissue by detecting thepresence of a polynucleotide encoding any of the various HPPDpolypeptides or active variants and fragments thereof. In oneembodiment, the detection method comprises assaying plant tissue usingPCR amplification.

As used herein, “primers” are isolated polynucleotides that are annealedto a complementary target DNA strand by nucleic acid hybridization toform a hybrid between the primer and the target DNA strand, thenextended along the target DNA strand by a polymerase, e.g., a DNApolymerase. Primer pairs of the disclosure refer to their use foramplification of a target polynucleotide, e.g., by the polymerase chainreaction (PCR) or other conventional nucleic-acid amplification methods.“PCR” or “polymerase chain reaction” is a technique used for theamplification of specific DNA segments (see, U.S. Pat. Nos. 4,683,195and 4,800,159; herein incorporated by reference).

Probes and primers are of sufficient nucleotide length to bind to thetarget DNA sequence and specifically detect and/or identify apolynucleotide encoding an HPPD polypeptide or active variant orfragment thereof as describe elsewhere herein. It is recognized that thehybridization conditions or reaction conditions can be determined by theoperator to achieve this result. This length may be of any length thatis of sufficient length to be useful in a detection method of choice.Such probes and primers can hybridize specifically to a target sequenceunder high stringency hybridization conditions. Probes and primersaccording to embodiments of the present disclosure may have complete DNAsequence identity of contiguous nucleotides with the target sequence,although probes differing from the target DNA sequence and that retainthe ability to specifically detect and/or identify a target DNA sequencemay be designed by conventional methods. Accordingly, probes and primerscan share about 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%,99% or greater sequence identity or complementarity to the targetpolynucleotide.

Methods for preparing and using probes and primers are described, forexample, in Molecular Cloning: A Laboratory Manual, 2.sup.nd ed, vol.1-3, ed. Sambrook et al., Cold Spring Harbor Laboratory Press, ColdSpring Harbor, N.Y. 1989 (hereinafter, “Sambrook et al., 1989”); CurrentProtocols in Molecular Biology, ed. Ausubel et al., Greene Publishingand Wiley-Interscience, New York, 1992 (with periodic updates)(hereinafter, “Ausubel et al., 1992”); and Innis et al., PCR Protocols:A Guide to Methods and Applications, Academic Press: San Diego, 1990.PCR primer pairs can be derived from a known sequence, for example, byusing computer programs intended for that purpose such as the PCR primeranalysis tool in Vector NTI version 10 (Invitrogen); PrimerSelect(DNASTAR Inc., Madison, Wis.); and Primer (Version 0.5.COPYRGT., 1991,Whitehead Institute for Biomedical Research, Cambridge, Mass.).Additionally, the sequence can be visually scanned and primers manuallyidentified using guidelines known to one of skill in the art.

D. Method of Identifying HPPD Variants.

Various methods can be employed to identify further HPPD variants. Thepolynucleotides of the disclosure are optionally used as substrates fora variety of diversity generating procedures, e.g., mutation,recombination and recursive recombination reactions, in addition totheir use in standard cloning methods as set forth in, e.g., Ausubel,Berger and Sambrook, i.e., to produce additional HPPD polynucleotidesand polypeptides with desired properties. A variety of diversitygenerating protocols can be used. The procedures can be used separately,and/or in combination to produce one or more variants of apolynucleotide or set of polynucleotides, as well variants of encodedproteins. Individually and collectively, these procedures providerobust, widely applicable ways of generating diversified polynucleotidesand sets of polynucleotides (including, e.g., polynucleotide libraries)useful, e.g., for the engineering or rapid evolution of polynucleotides,proteins, pathways, cells and/or organisms with new and/or improvedcharacteristics. The process of altering the sequence can result in, forexample, single nucleotide substitutions, multiple nucleotidesubstitutions, and insertion or deletion of regions of the nucleic acidsequence.

While distinctions and classifications are made in the course of theensuing discussion for clarity, it will be appreciated that thetechniques are often not mutually exclusive. Indeed, the various methodscan be used singly or in combination, in parallel or in series, toaccess diverse sequence variants.

The result of any of the diversity generating procedures describedherein can be the generation of one or more polynucleotides, which canbe selected or screened for polynucleotides that encode proteins with orwhich confer desirable properties. Following diversification by one ormore of the methods herein, or otherwise available to one of skill, anypolynucleotides that are produced can be selected for a desired activityor property, e.g. altered Km, use of alternative cofactors, increasedkcat, etc. This can include identifying any activity that can bedetected, for example, in an automated or automatable format, by any ofthe assays in the art. For example, modified HPPD polypeptides can bedetected by assaying for an increased insensitivity to HPPD inhibitor.Assays to measure such activity are described elsewhere herein. Avariety of related (or even unrelated) properties can be evaluated, inserial or in parallel, at the discretion of the practitioner.

Descriptions of a variety of diversity generating procedures, includingfamily shuffling and methods for generating modified nucleic acidsequences encoding multiple enzymatic domains, are found in thefollowing publications and the references cited therein: Soong N. et al.(2000) Nat Genet 25(4):436-39; Stemmer et al. (1999) Tumor Targeting4:1-4; Ness et al. (1999) Nature Biotechnology 17:893-896; Chang et al.(1999) Nature Biotechnology 17:793-797; Minshull and Stemmer (1999)Current Opinion in Chemical Biology 3:284-290; Christians et al. (1999)Nature Biotechnology 17:259-264; Crameri et al. (1998) Nature391:288-291; Crameri et al. (1997) Nature Biotechnology 15:436-438;Zhang et al. (1997) Proc. Natl. Acad. Sci. USA 94:4504-4509; Patten etal. (1997) Current Opinion in Biotechnology 8:724-733; Crameri et al.(1996) Nature Medicine 2:100-103; Crameri et al. (1996) NatureBiotechnology 14:315-319; Gates et al. (1996) Journal of MolecularBiology 255:373-386; Stemmer (1996) “Sexual PCR and Assembly PCR” In:The Encyclopedia of Molecular Biology. VCH Publishers, New York. pp.447-457; Crameri and Stemmer (1995) BioTechniques 18:194-195; Stemmer etal. (1995) Gene: 164:49-53; Stemmer (1995) Science 270: 1510; Stemmer(1995) Bio/Technology 13:549-553; Stemmer (1994) Nature 370:389-391; andStemmer (1994) Proc. Natl. Acad. Sci. USA 91:10747-10751. See alsoWO2008/073877 and US 20070204369, both of which are herein incorporatedby reference in their entirety.

Mutational methods of generating diversity include, for example,site-directed mutagenesis (Ling et al. (1997) Anal Biochem. 254(2):157-178; Dale et al. (1996) Methods Mol. Biol. 57:369-374; Smith (1985)Ann. Rev. Genet. 19:423-462; Botstein & Shortle (1985) Science229:1193-1201; Carter (1986) Biochem. J 237:1-7; and Kunkel (1987)Nucleic Acids & Molecular Biology (Eckstein, F. and Lilley, D. M. J.eds., Springer Verlag, Berlin)); mutagenesis using uracil containingtemplates (Kunkel (1985) Proc. Natl. Acad. Sci. USA 82:488-492; Kunkelet al. (1987) Methods in Enzymol. 154, 367-382; and Bass et al. (1988)Science 242:240-245); oligonucleotide-directed mutagenesis (Methods inEnzymol. 100: 468-500 (1983); Methods in Enzymol. 154: 329-350 (1987);Zoller & Smith (1982) Nucleic Acids Res. 10:6487-6500; Zoller & Smith(1983) Methods in Enzymol. 100:468-500; and Zoller & Smith (1987)Methods in Enzymol. 154:329-350); phosphorothioate-modified DNAmutagenesis (Taylor et al. (1985) Nucl. Acids Res. 13: 8749-8764; Tayloret al. (1985) Nucl. Acids Res. 13: 8765-8787 (1985); Nakamaye & Eckstein(1986) Nucl. Acids Res. 14: 9679-9698; Sayers et al. (1988) Nucl. AcidsRes. 16:791-802; and Sayers et al. (1988) Nucl. Acids Res. 16: 803-814);mutagenesis using gapped duplex DNA (Kramer et al. (1984) Nucl. AcidsRes. 12: 9441-9456; Kramer & Fritz (1987) Methods in Enzymol.154:350-367; Kramer et al. (1988) Nucl. Acids Res. 16: 7207; and Fritzet al. (1988) Nucl. Acids Res. 16: 6987-6999).

Additional suitable methods include, but are not limited to, pointmismatch repair (Kramer et al. (1984) Cell 38:879-887), mutagenesisusing repair-deficient host strains (Carter et al. (1985) Nucl. AcidsRes. 13: 4431-4443; and Carter (1987) Methods in Enzymol. 154: 382-403),deletion mutagenesis (Eghtedarzadeh & Henikoff (1986) Nucl. Acids Res.14: 5115), restriction-selection and restriction-purification (Wells etal. (1986) Phil. Trans. R. Soc. Lond. A 317: 415-423), mutagenesis bytotal gene synthesis (Nambiar et al. (1984) Science 223: 1299-1301;Sakamar and Khorana (1988) Nucl. Acids Res. 14: 6361-6372; Wells et al.(1985) Gene 34:315-323; and Grundström et al. (1985) Nucl. Acids Res.13: 3305-3316), and double-strand break repair (Mandecki (1986); Arnold(1993) Current Opinion in Biotechnology 4:450-455 and Proc. Natl. Acad.Sci. USA, 83:7177-7181). Additional details on many of the above methodscan be found in Methods in Enzymology Volume 154, which also describesuseful controls for trouble-shooting problems with various mutagenesismethods.

Additional details regarding various diversity generating methods can befound in the following U.S. patents, PCT publications, and EPOpublications: U.S. Pat. Nos. 5,605,793, 5,811,238, 5,830,721, 5,834,252,5,837,458, WO 95/22625, WO 96/33207, WO 97/20078, WO 97/35966, WO99/41402, WO 99/41383, WO 99/41369, WO 99/41368, EP 752008, EP 0932670,WO 99/23107, WO 99/21979, WO 98/31837, WO 98/27230, WO 98/13487, WO00/00632, WO 00/09679, WO 98/42832, WO 99/29902, WO 98/41653, WO98/41622, WO 98/42727, WO 00/18906, WO 00/04190, WO 00/42561, WO00/42559, WO 00/42560, WO 01/23401, and, PCT/US01/06775. See, alsoWO20074303, herein incorporated by reference.

In brief, several different general classes of sequence modificationmethods, such as mutation, recombination, etc. are applicable to thepresent disclosure and set forth, e.g., in the references above. Thatis, alterations to the component nucleic acid sequences to producedmodified gene fusion constructs can be performed by any number of theprotocols described, either before cojoining of the sequences, or afterthe cojoining step. The following exemplify some of the different typesof preferred formats for diversity generation in the context of thepresent disclosure, including, e.g., certain recombination baseddiversity generation formats.

Nucleic acids can be recombined in vitro by any of a variety oftechniques discussed in the references above, including e.g., DNAsedigestion of nucleic acids to be recombined followed by ligation and/orPCR reassembly of the nucleic acids. For example, sexual PCR mutagenesiscan be used in which random (or pseudo random, or even non-random)fragmentation of the DNA molecule is followed by recombination, based onsequence similarity, between DNA molecules with different but relatedDNA sequences, in vitro, followed by fixation of the crossover byextension in a polymerase chain reaction. This process and many processvariants are described in several of the references above, e.g., inStemmer (1994) Proc. Natl. Acad. Sci. USA 91:10747-10751.

Similarly, nucleic acids can be recursively recombined in vivo, e.g., byallowing recombination to occur between nucleic acids in cells. Manysuch in vivo recombination formats are set forth in the references notedabove. Such formats optionally provide direct recombination betweennucleic acids of interest, or provide recombination between vectors,viruses, plasmids, etc., comprising the nucleic acids of interest, aswell as other formats. Details regarding such procedures are found inthe references noted above.

Whole genome recombination methods can also be used in which wholegenomes of cells or other organisms are recombined, optionally includingspiking of the genomic recombination mixtures with desired librarycomponents (e.g., genes corresponding to the pathways of the presentdisclosure). These methods have many applications, including those inwhich the identity of a target gene is not known. Details on suchmethods are found, e.g., in WO 98/31837 and in PCT/US99/15972. Thus, anyof these processes and techniques for recombination, recursiverecombination, and whole genome recombination, alone or in combination,can be used to generate the modified nucleic acid sequences and/ormodified gene fusion constructs of the present disclosure.

Synthetic recombination methods can also be used, in whicholigonucleotides corresponding to targets of interest are synthesizedand reassembled in PCR or ligation reactions which includeoligonucleotides which correspond to more than one parental nucleicacid, thereby generating new recombined nucleic acids. Oligonucleotidescan be made by standard nucleotide addition methods, or can be made,e.g., by tri-nucleotide synthetic approaches. Details regarding suchapproaches are found in the references noted above, including, e.g., WO00/42561, WO 01/23401, WO 00/42560, and, WO 00/42559.

In silico methods of recombination can be affected in which geneticalgorithms are used in a computer to recombine sequence strings whichcorrespond to homologous (or even non-homologous) nucleic acids. Theresulting recombined sequence strings are optionally converted intonucleic acids by synthesis of nucleic acids which correspond to therecombined sequences, e.g., in concert with oligonucleotidesynthesis/gene reassembly techniques. This approach can generate random,partially random or designed variants. Many details regarding in silicorecombination, including the use of genetic algorithms, geneticoperators and the like in computer systems, combined with generation ofcorresponding nucleic acids (and/or proteins), as well as combinationsof designed nucleic acids and/or proteins (e.g., based on cross-oversite selection) as well as designed, pseudo-random or randomrecombination methods are described in WO 00/42560 and WO 00/42559.

Many methods of accessing natural diversity, e.g., by hybridization ofdiverse nucleic acids or nucleic acid fragments to single-strandedtemplates, followed by polymerization and/or ligation to regeneratefull-length sequences, optionally followed by degradation of thetemplates and recovery of the resulting modified nucleic acids can besimilarly used. In one method employing a single-stranded template, thefragment population derived from the genomic library(ies) is annealedwith partial, or, often approximately full length ssDNA or RNAcorresponding to the opposite strand. Assembly of complex chimeric genesfrom this population is then mediated by nuclease-base removal ofnon-hybridizing fragment ends, polymerization to fill gaps between suchfragments and subsequent single stranded ligation. The parentalpolynucleotide strand can be removed by digestion (e.g., if RNA oruracil-containing), magnetic separation under denaturing conditions (iflabeled in a manner conducive to such separation) and other availableseparation/purification methods. Alternatively, the parental strand isoptionally co-purified with the chimeric strands and removed duringsubsequent screening and processing steps. Additional details regardingthis approach are found, e.g., in PCT/US01/06775.

In another approach, single-stranded molecules are converted todouble-stranded DNA (dsDNA) and the dsDNA molecules are bound to a solidsupport by ligand-mediated binding. After separation of unbound DNA, theselected DNA molecules are released from the support and introduced intoa suitable host cell to generate a library enriched sequences whichhybridize to the probe. A library produced in this manner provides adesirable substrate for further diversification using any of theprocedures described herein.

Any of the preceding general recombination formats can be practiced in areiterative fashion (e.g., one or more cycles of mutation/recombinationor other diversity generation methods, optionally followed by one ormore selection methods) to generate a more diverse set of recombinantnucleic acids.

Mutagenesis employing polynucleotide chain termination methods have alsobeen proposed (see e.g., U.S. Pat. No. 5,965,408 and the referencesabove), and can be applied to the present disclosure. In this approach,double stranded DNAs corresponding to one or more genes sharing regionsof sequence similarity are combined and denatured, in the presence orabsence of primers specific for the gene. The single strandedpolynucleotides are then annealed and incubated in the presence of apolymerase and a chain terminating reagent (e.g., ultraviolet, gamma orX-ray irradiation; ethidium bromide or other intercalators; DNA bindingproteins, such as single strand binding proteins, transcriptionactivating factors, or histones; polycyclic aromatic hydrocarbons;trivalent chromium or a trivalent chromium salt; or abbreviatedpolymerization mediated by rapid thermocycling; and the like), resultingin the production of partial duplex molecules. The partial duplexmolecules, e.g., containing partially extended chains, are thendenatured and reannealed in subsequent rounds of replication or partialreplication resulting in polynucleotides which share varying degrees ofsequence similarity and which are diversified with respect to thestarting population of DNA molecules. Optionally, the products, orpartial pools of the products, can be amplified at one or more stages inthe process. Polynucleotides produced by a chain termination method,such as described above, are suitable substrates for any other describedrecombination format.

Diversity also can be generated in nucleic acids or populations ofnucleic acids using a recombinational procedure termed “incrementaltruncation for the creation of hybrid enzymes” (“ITCHY”) described inOstermeier et al. (1999) Nature Biotech 17:1205. This approach can beused to generate an initial a library of variants which can optionallyserve as a substrate for one or more in vitro or in vivo recombinationmethods. See, also, Ostermeier et al. (1999) Proc. Natl. Acad. Sci. USA,96: 3562-67; Ostermeier et al. (1999), Biological and MedicinalChemistry 7: 2139-44.

Mutational methods which result in the alteration of individualnucleotides or groups of contiguous or non-contiguous nucleotides can befavorably employed to introduce nucleotide diversity into the nucleicacid sequences and/or gene fusion constructs of the present disclosure.Many mutagenesis methods are found in the above-cited references;additional details regarding mutagenesis methods can be found infollowing, which can also be applied to the present disclosure.

For example, error-prone PCR can be used to generate nucleic acidvariants. Using this technique, PCR is performed under conditions wherethe copying fidelity of the DNA polymerase is low, such that a high rateof point mutations is obtained along the entire length of the PCRproduct. Examples of such techniques are found in the references aboveand, e.g., in Leung et al. (1989) Technique 1:11-15 and Caldwell et al.(1992) PCR Methods Applic. 2:28-33. Similarly, assembly PCR can be used,in a process which involves the assembly of a PCR product from a mixtureof small DNA fragments. A large number of different PCR reactions canoccur in parallel in the same reaction mixture, with the products of onereaction priming the products of another reaction.

Oligonucleotide directed mutagenesis can be used to introducesite-specific mutations in a nucleic acid sequence of interest. Examplesof such techniques are found in the references above and, e.g., inReidhaar-Olson et al. (1988) Science 241:53-57. Similarly, cassettemutagenesis can be used in a process that replaces a small region of adouble stranded DNA molecule with a synthetic oligonucleotide cassettethat differs from the native sequence. The oligonucleotide can contain,e.g., completely and/or partially randomized native sequence(s).

Recursive ensemble mutagenesis is a process in which an algorithm forprotein mutagenesis is used to produce diverse populations ofphenotypically related mutants, members of which differ in amino acidsequence. This method uses a feedback mechanism to monitor successiverounds of combinatorial cassette mutagenesis. Examples of this approachare found in Arkin & Youvan (1992) Proc. Natl. Acad. Sci. USA89:7811-7815.

Exponential ensemble mutagenesis can be used for generatingcombinatorial libraries with a high percentage of unique and functionalmutants. Small groups of residues in a sequence of interest arerandomized in parallel to identify, at each altered position, aminoacids which lead to functional proteins. Examples of such procedures arefound in Delegrave & Youvan (1993) Biotechnology Research 11:1548-1552.

In vivo mutagenesis can be used to generate random mutations in anycloned DNA of interest by propagating the DNA, e.g., in a strain of E.coli that carries mutations in one or more of the DNA repair pathways.These “mutator” strains have a higher random mutation rate than that ofa wild-type parent. Propagating the DNA in one of these strains willeventually generate random mutations within the DNA. Such procedures aredescribed in the references noted above.

Other procedures for introducing diversity into a genome, e.g. abacterial, fungal, animal or plant genome can be used in conjunctionwith the above described and/or referenced methods. For example, inaddition to the methods above, techniques have been proposed whichproduce nucleic acid multimers suitable for transformation into avariety of species (see, e.g., U.S. Pat. No. 5,756,316 and thereferences above). Transformation of a suitable host with suchmultimers, consisting of genes that are divergent with respect to oneanother, (e.g., derived from natural diversity or through application ofsite directed mutagenesis, error prone PCR, passage through mutagenicbacterial strains, and the like), provides a source of nucleic aciddiversity for DNA diversification, e.g., by an in vivo recombinationprocess as indicated above.

Alternatively, a multiplicity of monomeric polynucleotides sharingregions of partial sequence similarity can be transformed into a hostspecies and recombined in vivo by the host cell. Subsequent rounds ofcell division can be used to generate libraries, members of which,include a single, homogenous population, or pool of monomericpolynucleotides. Alternatively, the monomeric nucleic acid can berecovered by standard techniques, e.g., PCR and/or cloning, andrecombined in any of the recombination formats, including recursiverecombination formats, described above.

Methods for generating multispecies expression libraries have beendescribed (in addition to the reference noted above, see, e.g., U.S.Pat. Nos. 5,783,431 and 5,824,485) and their use to identify proteinactivities of interest has been proposed (In addition to the referencesnoted above, see, U.S. Pat. No. 5,958,672. Multispecies expressionlibraries include, in general, libraries comprising cDNA or genomicsequences from a plurality of species or strains, operably linked toappropriate regulatory sequences, in an expression cassette. The cDNAand/or genomic sequences are optionally randomly ligated to furtherenhance diversity. The vector can be a shuttle vector suitable fortransformation and expression in more than one species of host organism,e.g., bacterial species, eukaryotic cells. In some cases, the library isbiased by preselecting sequences which encode a protein of interest, orwhich hybridize to a nucleic acid of interest. Any such libraries can beprovided as substrates for any of the methods herein described.

The above described procedures have been largely directed to increasingnucleic acid and/or encoded protein diversity. However, in many cases,not all of the diversity is useful, e.g., functional, and contributesmerely to increasing the background of variants that must be screened orselected to identify the few favorable variants. In some applications,it is desirable to preselect or prescreen libraries (e.g., an amplifiedlibrary, a genomic library, a cDNA library, a normalized library, etc.)or other substrate nucleic acids prior to diversification, e.g., byrecombination-based mutagenesis procedures, or to otherwise bias thesubstrates towards nucleic acids that encode functional products. Forexample, in the case of antibody engineering, it is possible to bias thediversity generating process toward antibodies with functional antigenbinding sites by taking advantage of in vivo recombination events priorto manipulation by any of the described methods. For example, recombinedCDRs derived from B cell cDNA libraries can be amplified and assembledinto framework regions (e.g., Jirholt et al. (1998) Gene 215: 471) priorto diversifying according to any of the methods described herein.

Libraries can be biased towards nucleic acids which encode proteins withdesirable enzyme activities. For example, after identifying a variantfrom a library which exhibits a specified activity, the variant can bemutagenized using any known method for introducing DNA alterations. Alibrary comprising the mutagenized homologues is then screened for adesired activity, which can be the same as or different from theinitially specified activity. An example of such a procedure is proposedin U.S. Pat. No. 5,939,250. Desired activities can be identified by anymethod known in the art. For example, WO 99/10539 proposes that genelibraries can be screened by combining extracts from the gene librarywith components obtained from metabolically rich cells and identifyingcombinations which exhibit the desired activity. It has also beenproposed (e.g., WO 98/58085) that clones with desired activities can beidentified by inserting bioactive substrates into samples of thelibrary, and detecting bioactive fluorescence corresponding to theproduct of a desired activity using a fluorescent analyzer, e.g., a flowcytometry device, a CCD, a fluorometer, or a spectrophotometer.

Libraries can also be biased towards nucleic acids which have specifiedcharacteristics, e.g., hybridization to a selected nucleic acid probe.For example, application WO 99/10539 proposes that polynucleotidesencoding a desired activity (e.g., an enzymatic activity, for example: alipase, an esterase, a protease, a glycosidase, a glycosyl transferase,a phosphatase, a kinase, an oxygenase, a peroxidase, a hydrolase, ahydratase, a nitrilase, a transaminase, an amidase or an acylase) can beidentified from among genomic DNA sequences in the following manner.Single stranded DNA molecules from a population of genomic DNA arehybridized to a ligand-conjugated probe. The genomic DNA can be derivedfrom either a cultivated or uncultivated microorganism, or from anenvironmental sample. Alternatively, the genomic DNA can be derived froma multicellular organism, or a tissue derived there from. Second strandsynthesis can be conducted directly from the hybridization probe used inthe capture, with or without prior release from the capture medium or bya wide variety of other strategies known in the art. Alternatively, theisolated single-stranded genomic DNA population can be fragmentedwithout further cloning and used directly in, e.g., arecombination-based approach, that employs a single-stranded template,as described above.

“Non-Stochastic” methods of generating nucleic acids and polypeptidesare found in WO 00/46344. These methods, including proposednon-stochastic polynucleotide reassembly and site-saturation mutagenesismethods be applied to the present disclosure as well. Random orsemi-random mutagenesis using doped or degenerate oligonucleotides isalso described in, e.g., Arkin and Youvan (1992) Biotechnology10:297-300; Reidhaar-Olson et al. (1991) Methods Enzymol. 208:564-86;Lim and Sauer (1991) J. Mol. Biol. 219:359-76; Breyer and Sauer (1989)J. Biol. Chem. 264:13355-60); and U.S. Pat. Nos. 5,830,650 and5,798,208, and EP Patent 0527809 B1.

It will readily be appreciated that any of the above describedtechniques suitable for enriching a library prior to diversification canalso be used to screen the products, or libraries of products, producedby the diversity generating methods. Any of the above described methodscan be practiced recursively or in combination to alter nucleic acids,e.g., HPPD encoding polynucleotides.

The above references provide many mutational formats, includingrecombination, recursive recombination, recursive mutation andcombinations or recombination with other forms of mutagenesis, as wellas many modifications of these formats. Regardless of the diversitygeneration format that is used, the nucleic acids of the presentdisclosure can be recombined (with each other, or with related (or evenunrelated) sequences) to produce a diverse set of recombinant nucleicacids for use in the gene fusion constructs and modified gene fusionconstructs of the present disclosure, including, e.g., sets ofhomologous nucleic acids, as well as corresponding polypeptides.

Many of the above-described methodologies for generating modifiedpolynucleotides generate a large number of diverse variants of aparental sequence or sequences. In some embodiments, the modificationtechnique (e.g., some form of shuffling) is used to generate a libraryof variants that is then screened for a modified polynucleotide or poolof modified polynucleotides encoding some desired functional attribute,e.g., improved HPPD inhibitor insensitivity and/or maintained orimproved HPPD activity.

One example of selection for a desired enzymatic activity entailsgrowing host cells under conditions that inhibit the growth and/orsurvival of cells that do not sufficiently express an enzymatic activityof interest, e.g. the HPPD activity. Using such a selection process caneliminate from consideration all modified polynucleotides except thoseencoding a desired enzymatic activity. For example, in some embodimentsof the disclosed host cells are maintained under conditions that inhibitcell growth or survival in the absence of sufficient levels of HPPD,e.g., a concentration of an HPPD inhibitor that is lethal or inhibitsthe growth of a wild-type plant of the same variety that lacks or doesnot express the HPPD polynucleotide or active variant or fragmentthereof. Under these conditions, only a host cell harboring a modifiednucleic acid that encodes enzymatic activity or activities able tocatalyze production of sufficient levels of the product will survive andgrow. Some embodiments of the disclosure employ multiples rounds ofscreening at increasing concentrations of an HPPD inhibitor.

For convenience and high throughput it will often be desirable toscreen/select for desired modified nucleic acids in a microorganism,e.g., a bacteria such as E. coli. On the other hand, screening in plantcells or plants can in some cases be preferable where the ultimate aimis to generate a modified nucleic acid for expression in a plant system.

In some preferred embodiments of the disclosure throughput is increasedby screening pools of host cells expressing different modified nucleicacids, either alone or as part of a gene fusion construct. Any poolsshowing significant activity can be deconvoluted to identify singlevariants expressing the desirable activity.

In high throughput assays, it is possible to screen up to severalthousand different variants in a single day. For example, each well of amicrotiter plate can be used to run a separate assay, or, ifconcentration or incubation time effects are to be observed, every 5-10wells can test a single variant.

In addition to fluidic approaches, it is possible, as mentioned above,simply to grow cells on media plates that select for the desiredenzymatic or metabolic function. This approach offers a simple andhigh-throughput screening method.

A number of well known robotic systems have also been developed forsolution phase chemistries useful in assay systems. These systemsinclude automated workstations like the automated synthesis apparatusdeveloped by Takeda Chemical Industries, LTD. (Osaka, Japan) and manyrobotic systems utilizing robotic arms (Zymate II, Zymark Corporation,Hopkinton, Mass.; Orca, Hewlett-Packard, Palo Alto, Calif.) which mimicthe manual synthetic operations performed by a scientist. Any of theabove devices are suitable for application to the present disclosure.The nature and implementation of modifications to these devices (if any)so that they can operate as discussed herein with reference to theintegrated system will be apparent to persons skilled in the relevantart.

High throughput screening systems are commercially available (see, e.g.,Zymark Corp., Hopkinton, Mass.; Air Technical Industries, Mentor, Ohio;Beckman Instruments, Inc. Fullerton, Calif.; Precision Systems, Inc.,Natick, Mass., etc.). These systems typically automate entire proceduresincluding all sample and reagent pipetting, liquid dispensing, timedincubations, and final readings of the microplate in detector(s)appropriate for the assay. These configurable systems provide highthroughput and rapid start up as well as a high degree of flexibilityand customization.

The manufacturers of such systems provide detailed protocols for thevarious high throughput devices. Thus, for example, Zymark Corp.provides technical bulletins describing screening systems for detectingthe modulation of gene transcription, ligand binding, and the like.Microfluidic approaches to reagent manipulation have also beendeveloped, e.g., by Caliper Technologies (Mountain View, Calif.).

Non-Limiting Embodiments Include:

1. A recombinant polypeptide having 4-hydroxyphenylpyruvate dioxygenase(HPPD) activity; wherein the polypeptide having 4-hydroxyphenylpyruvatedioxygenase activity comprises:

(SEQ ID NO: 80)                5                   10                  15Met Gly Pro Thr Pro Thr Ala Thr Ala Ala Gly Ala Ala Val Ala                20                  25                  30Ala Ala Ser Ala Ala Glu Gln Ala Ala Phe Arg Leu Val Gly His                35                  40                  45Arg Asn Phe Val Arg Phe Asn Pro Arg Ser Asp Arg Phe Gln Thr                50                  55                  60Leu Ala Phe His His Val Xaa Xaa Xaa Xaa Xaa Asp Xaa Ala Ser                65                  70                  75Ala Ala Gly Arg Phe Ser Phe Ala Leu Gly Val Pro Leu Ala Ala                80                  85                  90Arg Ser Asp Leu Ser Thr Gly Asn Ser Ala His Ala Ser Leu Leu                95                  100                 105Leu Arg Ser Gly Ser Leu Ser Leu Leu Phe Thr Ala Pro Tyr Ala                110                 115                 120His Gly Ala Asp Ala Ala Thr Ala Ala Leu Pro Ser Phe Ser Ala                125                 130                 135Ala Ala Ala Arg Xaa Phe Ala Ala Asp His Gly Leu Ala Val Arg                140                 145                 150Ala Val Ala Leu Arg Val Ala Asp Ala Glu Asp Xaa Xaa Xaa Ala                155                 160                 165Ser Xaa Xaa Xaa Gly Ala Xaa Xaa Xaa Xaa Xaa Xaa Xaa Xaa Xaa                170                 175                 180Xaa Xaa Gly Xaa Xaa Xaa Xaa Xaa Xaa Xaa Xaa Tyr Gly Asp Val                185                 190                 195Xaa Xaa Arg Tyr Val Ser Xaa Xaa Xaa Xaa Xaa Xaa Xaa Xaa Xaa                200                 205                 210Xaa Leu Pro Gly Xaa Glu Xaa Val Xaa Xaa Xaa Xaa Xaa Xaa Xaa                215                 220                 225Xaa Xaa Xaa Xaa Xaa Phe Xaa His Ile Xaa Xaa Xaa Val Pro Glu                230                 235                 240Leu Xaa Pro Xaa Xaa Xaa Tyr Xaa Xaa Gly Phe Thr Xaa Phe Xaa                245                 250                 255Xaa Xaa Ala Glu Phe Thr Thr Glu Asp Val Gly Thr Thr Glu Ser                260                 265                 270Gly Leu Asn Ser Met Ala Leu Ala Asn Asn Ser Glu Asn Val Leu                275                 280                 285Leu Pro Xaa Asn Glu Pro Val His Gly Thr Lys Arg Arg Ser Gln                290                 295                 300Ile Gln Thr Phe Leu Asp Xaa His Gly Gly Pro Gly Val Gln His                305                 310                 315Ile Ala Leu Ala Ser Asp Asp Val Leu Arg Thr Leu Arg Glu Met                320                 325                 330Arg Ala Arg Ser Ala Met Gly Gly Phe Glu Phe Leu Pro Pro Pro                335                 340                 345Xaa Xaa Asp Tyr Tyr Asp Gly Val Xaa Xaa Cys Xaa Xaa Asp Xaa                350                 355                 360Leu Xaa Xaa Xaa Gln Xaa Xaa Xaa Cys Gln Xaa Xaa Xaa Val Xaa                365                 370                 375Val Asp Arg Xaa Xaa Xaa Gly Xaa Xaa Leu Gln Xaa Xaa Thr Xaa                380                 385                 390Xaa Xaa Gly Xaa Arg Xaa Xaa Xaa Xaa Xaa Xaa Xaa Xaa Xaa Xaa                395                 400                 405Xaa Xaa Cys Xaa Xaa Xaa Xaa Xaa Xaa Xaa Xaa Glu Tyr Gln Lys                410                 415                 420Xaa Xaa Xaa Gly Gly Xaa Gly Xaa Gly Xaa Xaa Xaa Xaa Leu Phe                425                 430                 435Lys Xaa Xaa Xaa Xaa Xaa Xaa Xaa Xaa Xaa Xaa Xaa Xaa Xaa Ala                440 Ala Xaa Xaa Xaa Thr Ala Gln Gly Ser;

-   -   wherein        -   Xaa at position 52 is Glu, Asp, Gly, His, Arg, Ser or Thr;        -   Xaa at position 53 is Leu, Phe, Ile or Met;        -   Xaa at position 54 is Trp, Cys, Leu or Gln;        -   Xaa at position 55 is Cys, Ala, Gly, Thr or Val;        -   Xaa at position 56 is Ala, His, Leu, Asn, Gln, Ser or Thr;        -   Xaa at position 58 is Ala, Gly or Thr;        -   Xaa at position 125 is Arg or Leu;        -   Xaa at position 147 is Ala or Ser;        -   Xaa at position 148 is Phe, Trp or Tyr;        -   Xaa at position 149 is Arg, Ala, Ile, Lys, Met, Pro, Ser,            Thr, Val or Trp;        -   Xaa at position 152 is Val or Glu;        -   Xaa at position 153 is Ala, Phe, Ile, Lys, Leu, Gln, Arg,            Thr or Val;        -   Xaa at position 154 is Ala, Cys, Gly, Asn, Arg or Thr;        -   Xaa at position 157 is Arg, His, Asn, Thr or Val;        -   Xaa at position 158 is Pro, Ala, Glu, Gly or Lys;        -   Xaa at position 159 is Ala, Cys, Met, Ser, Thr or Val;        -   Xaa at position 160 is Phe, Leu, Met or Tyr;        -   Xaa at position 161 is Gly, Ala, Glu, Leu, Met, Asn, Pro,            Gln, Arg, Ser, Thr, Trp or Tyr;        -   Xaa at position 162 is Pro or Thr;        -   Xaa at position 163 is Val, Ala, Cys, Met or Thr;        -   Xaa at position 164 is Asp, Ala, Glu, His, Ser or Thr;        -   Xaa at position 165 is Leu, Cys, Met or Val;        -   Xaa at position 166 is Gly, Ala or Pro;        -   Xaa at position 167 is Arg or Val;        -   Xaa at position 169 is Phe, Ala, His, Trp or Tyr;        -   Xaa at position 170 is Arg, Cys, Gly, Ile, Lys, Leu, Met,            Pro, Gln, Ser, Thr, Val or Trp;        -   Xaa at position 171 is Leu, Phe, Ile, Met or Val;        -   Xaa at position 172 is Ala, Pro, Arg or Ser;        -   Xaa at position 173 is Glu or Pro;        -   Xaa at position 174 is Val, Cys or Ile;        -   Xaa at position 175 is Glu, Asp, Val or Trp;        -   Xaa at position 176 is Leu, Ala or Met;        -   Xaa at position 181 is Val, Phe, Ile, Met or Asn;        -   Xaa at position 182 is Leu or Met;        -   Xaa at position 187 is Tyr, Cys, Glu, Gly, His, Met or Val;        -   Xaa at position 188 is Pro, Asp, Gly or Gln;        -   Xaa at position 189 is Asp, Glu, Pro, Ser or Thr;        -   Xaa at position 190 is Gly, Ala, Cys, Asp, Glu, Leu, Met,            Asn, Pro, Gln, Arg, Ser, Thr, Val or Trp;        -   Xaa at position 191 is Ala, Glu, Phe, Gly, His, Ile, Lys,            Leu, Met, Asn, Arg, Ser, Thr or Val;        -   Xaa at position 192 is Ala or Val;        -   Xaa at position 193 is Gly, Ala, His, Ile, Leu, Pro, Gln,            Arg, Ser, Thr or Val;        -   Xaa at position 194 is Glu, Asp or Leu;        -   Xaa at position 195 is Pro, Ala, Cys, Asp, Glu, Gln, Ser,            Thr or Val;        -   Xaa at position 196 is Phe or Trp;        -   Xaa at position 200 is Phe or Cys;        -   Xaa at position 202 is Gly, Ala, Glu, Lys, Leu, Thr, Val or            Tyr;        -   Xaa at position 204 is Ala, Cys, Asp, Glu, Gly, His, Lys,            Leu, Met, Asn, Gln, Thr or Val;        -   Xaa at position 205 is Ser, Asp, Gly, Leu, Gln, Thr or Val;        -   Xaa at position 206 is Pro, Cys, Asp, Lys, Leu, Gln, Ser or            Thr;        -   Xaa at position 207 is Gly, Gln, Ser or Val;        -   Xaa at position 208 is Ala, Gly, His, Gln, Arg or Trp;        -   Xaa at position 209 is Ala, Cys, Asp, Glu, Gly, Ile, Lys,            Leu, Met, Pro, Gln, Ser, Thr or Trp;        -   Xaa at position 210 is Asp, Glu, Gly, Ser or Thr;        -   Xaa at position 211 is Tyr, Cys, Phe, Leu, Ser or Trp;        -   Xaa at position 212 is Gly or Lys;        -   Xaa at position 213 is Leu or Trp;        -   Xaa at position 214 is Ser, Lys, Met, Asn, Gln, Arg or Thr;        -   Xaa at position 215 is Arg, Ala or Gly;        -   Xaa at position 217 is Asp, Gln or Tyr;        -   Xaa at position 220 is Val or Thr;        -   Xaa at position 221 is Gly, Ala, Phe, His, Ile, Leu, Met,            Thr or Val;        -   Xaa at position 222 is Asn, Gly or Val;        -   Xaa at position 227 is Ala, Asp, Glu, Gly, Ile, Lys, Leu,            Met, Asn, Gln, Arg, Ser, Thr or Val;        -   Xaa at position 229 is Ala or Thr;        -   Xaa at position 230 is Ala, Arg or Val;        -   Xaa at position 231 is Ala, Cys, His, Leu, Ser or Thr;        -   Xaa at position 233 is Met or Val;        -   Xaa at position 234 is Ala, Cys, Glu, Gly, Lys, Leu, Met,            Gln, Ser or Val;        -   Xaa at position 238 is Gly or Ser;        -   Xaa at position 240 is His or Arg;        -   Xaa at position 241 is Glu, Ala, Asp, Gly, Asn, Pro, Arg,            Ser or Thr;        -   Xaa at position 242 is Phe, Ala, Asp or Ser;        -   Xaa at position 273 is Leu or Val;        -   Xaa at position 292 is His or Asn;        -   Xaa at position 331 is Leu, Asp, Gly, Asn or Arg;        -   Xaa at position 332 is Ser or Ala;        -   Xaa at position 339 is Arg or Lys;        -   Xaa at position 340 is Arg, Glu, Lys or Asn;        -   Xaa at position 342 is Ala, Cys, Leu, Met, Asn, Arg or Val;        -   Xaa at position 343 is Gly or Arg;        -   Xaa at position 345 is Val or Ile;        -   Xaa at position 347 is Thr or Ser;        -   Xaa at position 348 is Glu or Tyr;        -   Xaa at position 349 is Ala, Glu, Gln, Arg or Ser;        -   Xaa at position 351 is Ile, Cys or Val;        -   Xaa at position 352 is Asn, Glu, Lys, Leu, Gln or Arg;        -   Xaa at position 353 is Glu, Leu, Met, Ser or Thr;        -   Xaa at position 356 is Glu, Lys or Arg;        -   Xaa at position 357 is Leu or Tyr;        -   Xaa at position 358 is Gly, Glu or Arg;        -   Xaa at position 360 is Met, Leu or Thr;        -   Xaa at position 364 is Asp, Gly, Ser or Val;        -   Xaa at position 365 is Asp or Ala;        -   Xaa at position 366 is Gln or Glu;        -   Xaa at position 368 is Val or Leu;        -   Xaa at position 369 is Leu, Met or Val;        -   Xaa at position 372 is Ile, Ala, Lys, Gln, Ser or Thr;        -   Xaa at position 373 is Phe, Gly, Leu, Arg or Val;        -   Xaa at position 375 is Lys, Leu or Arg;        -   Xaa at position 376 is Pro, Cys, Gly, Ser, Val or Trp;        -   Xaa at position 377 is Val, Glu, Gly or Leu;        -   Xaa at position 379 is Asp or Lys;        -   Xaa at position 381 is Pro or Asn;        -   Xaa at position 382 is Thr, Ala, Phe or Ser;        -   Xaa at position 383 is Phe, Leu or Met;        -   Xaa at position 384 is Phe, Trp or Tyr;        -   Xaa at position 385 is Leu, Ile or Val;        -   Xaa at position 386 is Glu, Cys, Ile or Val;        -   Xaa at position 387 is Ile, Gly or Leu;        -   Xaa at position 388 is Ile, Leu, Ser or Val;        -   Xaa at position 389 is Gln, Gly, Lys or Thr;        -   Xaa at position 390 is Arg or Asn;        -   Xaa at position 391 is Ile, Leu or Val;        -   Xaa at position 392 is Gly, Arg or Val;        -   Xaa at position 394 is Met, Ile, Lys, Leu, Gln, Val or Tyr;        -   Xaa at position 395 is Glu, Lys, Gln, Ser or Val;        -   Xaa at position 396 is Lys, Ala, Leu, Met, Gln, Arg, Thr or            Val;        -   Xaa at position 397 is Asp, Gly or Ser;        -   Xaa at position 398 is Glu, Ala, Asp, Gly, Pro or Ser;        -   Xaa at position 399 is Lys, Ala, Asp, Gly, His, Ile, Met,            Asn, Gln, Arg, Ser, Thr, Val or Tyr;        -   Xaa at position 400 is Gly, Glu, Lys or Ser;        -   Xaa at position 401 is Gln, Ala, Glu, Ser or Val;        -   Xaa at position 406 is Gly or Cys;        -   Xaa at position 407 is Gly, Ala, Lys, Leu, Arg, Ser or Thr;        -   Xaa at position 408 is Cys, Gly, Arg, Thr, Val or Trp;        -   Xaa at position 411 is Phe, Ala or Leu;        -   Xaa at position 413 is Lys, Ala, Pro, Arg or Ser;        -   Xaa at position 415 is Asn or Ala;        -   Xaa at position 416 is Phe, Arg or Val;        -   Xaa at position 417 is Gly, Gln or Ser;        -   Xaa at position 418 is Gln, Ala, Cys, Glu, Gly, Leu or Thr;        -   Xaa at position 422 is Ser or Met;        -   Xaa at position 423 is Ile, Val or Trp;        -   Xaa at position 424 is Glu or Gln;        -   Xaa at position 425 is Asp, Ala, Glu, Gly, Met, Ser or Thr;        -   Xaa at position 426 is Tyr, Leu or Trp;        -   Xaa at position 427 is Glu, Ala, Leu or Met;        -   Xaa at position 428 is Lys, Arg or Val;        -   Xaa at position 429 is Ser, Cys, Asp, Gly or Thr;        -   Xaa at position 430 is Leu, Met or Val;        -   Xaa at position 431 is Glu, Ala, Phe, Gly, Leu or Asn;        -   Xaa at position 432 is Ala, Asp, Gly, Lys, Leu, Arg, Ser or            Val;        -   Xaa at position 433 is Lys, Glu, His, Leu, Pro, Arg, Ser or            Val;        -   Xaa at position 434 is Gln, Ala, Cys, Asp, Phe, Gly, His,            Lys, Leu or Arg;        -   Xaa at position 437 is Ala, Phe, Lys or Val;        -   Xaa at position 438 is Ala, Gly or Arg;        -   Xaa at position 439 is Ala or Arg;    -   wherein one or more amino acid(s) designated by Xaa in SEQ ID        NO:80 is an amino acid different from the corresponding amino        acid of SEQ ID NO: 1; and wherein the polypeptide having        4-hydroxyphenylpyruvate dioxygenase activity has improved        insensitivity to an HPPD inhibitor compared to the polypeptide        of SEQ ID NO: 1.

2. A recombinant polypeptide having 4-hydroxyphenylpyruvate dioxygenase(HPPD) activity; wherein the polypeptide having 4-hydroxyphenylpyruvatedioxygenase activity comprises:

(SEQ ID NO: 81)                5                   10                  15Met Gly Pro Thr Pro Thr Ala Thr Ala Ala Gly Ala Ala Val Ala                20                  25                  30Ala Ala Ser Ala Ala Glu Gln Ala Ala Phe Arg Leu Val Gly His                35                  40                  45Arg Asn Phe Val Arg Phe Asn Pro Arg Ser Asp Arg Phe Gln Thr                50                  55                  60Leu Ala Phe His His Val Glu Xaa Trp Cys Xaa Asp Ala Ala Ser                65                  70                  75Ala Ala Gly Arg Phe Ser Phe Ala Leu Gly Val Pro Leu Ala Ala                80                  85                  90Arg Ser Asp Leu Ser Thr Gly Asn Ser Ala His Ala Ser Leu Leu                95                  100                 105Leu Arg Ser Gly Ser Leu Ser Leu Leu Phe Thr Ala Pro Tyr Ala                110                 115                 120His Gly Ala Asp Ala Ala Thr Ala Ala Leu Pro Ser Phe Ser Ala                125                 130                 135Ala Ala Ala Arg Xaa Phe Ala Ala Asp His Gly Leu Ala Val Arg                140                 145                 150Ala Val Ala Leu Arg Val Ala Asp Ala Glu Asp Ala Phe Arg Ala                155                 160                 165Ser Val Ala Ala Gly Ala Arg Xaa Xaa Phe Xaa Pro Val Asp Leu                170                 175                 180Xaa Arg Gly Xaa Arg Xaa Ala Glu Val Glu Leu Tyr Gly Asp Val                185                 190                 195Val Xaa Arg Tyr Val Ser Tyr Pro Xaa Xaa Xaa Ala Xaa Glu Pro                200                 205                 210Phe Leu Pro Gly Phe Glu Gly Val Ala Ser Xaa Gly Ala Ala Asp                215                 220                 225Xaa Gly Leu Xaa Xaa Phe Xaa His Ile Val Xaa Asn Val Pro Glu                230                 235                 240Leu Xaa Pro Ala Ala Ala Tyr Met Ala Gly Phe Thr Gly Phe His                245                 250                 255Glu Phe Ala Glu Phe Thr Thr Glu Asp Val Gly Thr Thr Glu Ser                260                 265                 270Gly Leu Asn Ser Met Ala Leu Ala Asn Asn Ser Glu Asn Val Leu                275                 280                 285Leu Pro Leu Asn Glu Pro Val His Gly Thr Lys Arg Arg Ser Gln                290                 295                 300Ile Gln Thr Phe Leu Asp His His Gly Gly Pro Gly Val Gln His                305                 310                 315Ile Ala Leu Ala Ser Asp Asp Val Leu Arg Thr Leu Arg Glu Met                320                 325                 330Arg Ala Arg Ser Ala Met Gly Gly Phe Glu Phe Leu Pro Pro Pro                335                 340                 345Xaa Xaa Asp Tyr Tyr Asp Gly Val Arg Xaa Cys Xaa Gly Asp Val                350                 355                 360Leu Thr Glu Xaa Gln Ile Xaa Glu Cys Gln Xaa Leu Xaa Val Xaa                365                 370                 375Val Asp Arg Asp Asp Xaa Gly Val Leu Leu Gln Ile Xaa Thr Xaa                380                 385                 390Xaa Val Gly Asp Arg Xaa Xaa Xaa Phe Xaa Glu Xaa Ile Gln Xaa                395                 400                 405Ile Gly Cys Met Glu Xaa Asp Xaa Xaa Gly Gln Glu Tyr Gln Lys                410                 415                 420Gly Gly Cys Gly Gly Phe Gly Xaa Gly Asn Phe Xaa Xaa Leu Phe                425                 430                 435Lys Ser Xaa Glu Asp Tyr Glu Lys Xaa Leu Xaa Xaa Lys Xaa Ala                440 Ala Xaa Xaa Xaa Thr Ala Gln Gly Ser;

-   -   wherein        -   Xaa at position 53 is Leu or Phe;        -   Xaa at position 56 is Ala or Ser;        -   Xaa at position 125 is Arg or Leu;        -   Xaa at position 158 is Pro or Lys;        -   Xaa at position 159 is Ala or Cys;        -   Xaa at position 161 is Gly, Glu, Gln, Ser, Tyr, Asn or Leu;        -   Xaa at position 166 is Gly, Pro or Ala;        -   Xaa at position 169 is Phe or His;        -   Xaa at position 171 is Leu or Phe;        -   Xaa at position 182 is Leu or Met;        -   Xaa at position 189 is Asp or Pro;        -   Xaa at position 190 is Gly or Thr;        -   Xaa at position 191 is Ala, Ser, Leu or Gly;        -   Xaa at position 193 is Gly or Gln;        -   Xaa at position 206 is Pro, Gln, Ser, Lys or Leu;        -   Xaa at position 211 is Tyr, Leu or Ser;        -   Xaa at position 214 is Ser, Asn, Thr, Arg or Met;        -   Xaa at position 215 is Arg or Gly;        -   Xaa at position 217 is Asp or Tyr;        -   Xaa at position 221 is Gly, Val or Ala;        -   Xaa at position 227 is Ala or Gly;        -   Xaa at position 331 is Leu, Asn, Arg, Gly or Asp;        -   Xaa at position 332 is Ser or Ala;        -   Xaa at position 340 is Arg or Lys;        -   Xaa at position 342 is Ala, Val, Met or Cys;        -   Xaa at position 349 is Ala, Gln or Glu;        -   Xaa at position 352 is Asn or Arg;        -   Xaa at position 356 is Glu, Lys or Arg;        -   Xaa at position 358 is Gly or Glu;        -   Xaa at position 360 is Met or Leu;        -   Xaa at position 366 is Gln or Glu;        -   Xaa at position 373 is Phe or Val;        -   Xaa at position 375 is Lys, Leu or Arg;        -   Xaa at position 376 is Pro or Trp;        -   Xaa at position 381 is Pro or Asn;        -   Xaa at position 382 is Thr or Ser;        -   Xaa at position 383 is Phe, Met or Leu;        -   Xaa at position 385 is Leu, Val or Ile;        -   Xaa at position 387 is Ile or Leu;        -   Xaa at position 390 is Arg or Asn;        -   Xaa at position 396 is Lys, Thr, Met or Leu;        -   Xaa at position 398 is Glu, Asp or Ala;        -   Xaa at position 399 is Lys, Asn, Arg, Gln or Ser;        -   Xaa at position 413 is Lys or Ala;        -   Xaa at position 417 is Gly, Ser or Gln;        -   Xaa at position 418 is Gln or Glu;        -   Xaa at position 423 is Ile or Trp;        -   Xaa at position 429 is Ser, Gly or Thr;        -   Xaa at position 431 is Glu or Phe;        -   Xaa at position 432 is Ala, Arg, Lys or Ser;        -   Xaa at position 434 is Gln, Arg, His, Leu or Lys;        -   Xaa at position 437 is Ala, Lys or Phe;        -   Xaa at position 438 is Ala, Gly or Arg;        -   Xaa at position 439 is Ala or Arg;    -   wherein one or more amino acid(s) designated by Xaa in SEQ ID        NO:81 is an amino acid different from the corresponding amino        acid of SEQ ID NO: 1; and wherein the polypeptide having        4-hydroxyphenylpyruvate dioxygenase activity has improved        insensitivity to an HPPD inhibitor compared to the polypeptide        of SEQ ID NO: 1.

3. A recombinant polypeptide having 4-hydroxyphenylpyruvate dioxygenase(HPPD) activity; wherein the polypeptide having 4-hydroxyphenylpyruvatedioxygenase activity comprises:

(SEQ ID NO: 82)                5                   10                  15Met Gly Pro Thr Pro Thr Ala Thr Ala Ala Gly Ala Ala Val Ala                20                  25                  30Ala Ala Ser Ala Ala Glu Gln Ala Ala Phe Arg Leu Val Gly His                35                  40                  45Arg Asn Phe Val Arg Phe Asn Pro Arg Ser Asp Arg Phe Gln Thr                50                  55                  60Leu Ala Phe His His Val Glu Leu Trp Cys Ala Asp Ala Ala Ser                65                  70                  75Ala Ala Gly Arg Phe Ser Phe Ala Leu Gly Val Pro Leu Ala Ala                80                  85                  90Arg Ser Asp Leu Ser Thr Gly Asn Ser Ala His Ala Ser Leu Leu                95                  100                 105Leu Arg Ser Gly Ser Leu Ser Leu Leu Phe Thr Ala Pro Tyr Ala                110                 115                 120His Gly Ala Asp Ala Ala Thr Ala Ala Leu Pro Ser Phe Ser Ala                125                 130                 135Ala Ala Ala Arg Arg Phe Ala Ala Asp His Gly Leu Ala Val Arg                140                 145                 150Ala Val Ala Leu Arg Val Ala Asp Ala Glu Asp Ala Phe Arg Ala                155                 160                 165Ser Val Ala Ala Gly Ala Arg Xaa Ala Phe Gly Pro Val Asp Leu                170                 175                 180Gly Arg Gly Phe Arg Leu Ala Glu Val Glu Leu Tyr Gly Asp Val                185                 190                 195Val Xaa Arg Tyr Val Ser Tyr Pro Xaa Gly Xaa Ala Gly Glu Pro                200                 205                 210Phe Leu Pro Gly Phe Glu Gly Val Ala Xaa Xaa Gly Ala Ala Asp                215                 220                 225Xaa Gly Leu Xaa Arg Phe Asp His Ile Val Gly Asn Val Pro Glu                230                 235                 240Leu Xaa Pro Ala Ala Ala Tyr Met Ala Gly Phe Thr Gly Phe His                245                 250                 255Glu Phe Ala Glu Phe Thr Thr Glu Asp Val Gly Thr Thr Glu Ser                260                 265                 270Gly Leu Asn Ser Met Ala Leu Ala Asn Asn Ser Glu Asn Val Leu                275                 280                 285Leu Pro Leu Asn Glu Pro Val His Gly Thr Lys Arg Arg Ser Gln                290                 295                 300Ile Gln Thr Phe Leu Asp His His Gly Gly Pro Gly Val Gln His                305                 310                 315Ile Ala Leu Ala Ser Asp Asp Val Leu Arg Thr Leu Arg Glu Met                320                 325                 330Arg Ala Arg Ser Ala Met Gly Gly Phe Glu Phe Leu Pro Pro Pro                335                 340                 345Leu Ser Asp Tyr Tyr Asp Gly Val Arg Xaa Cys Xaa Gly Asp Val                350                 355                 360Leu Thr Glu Ala Gln Ile Asn Glu Cys Gln Xaa Leu Gly Val Xaa                365                 370                 375Val Asp Arg Asp Asp Xaa Gly Val Leu Leu Gln Ile Phe Thr Lys                380                 385                 390Xaa Val Gly Asp Arg Pro Thr Phe Phe Xaa Glu Xaa Ile Gln Xaa                395                 400                 405Ile Gly Cys Met Glu Lys Asp Glu Lys Gly Gln Glu Tyr Gln Lys                410                 415                 420Gly Gly Cys Gly Gly Phe Gly Lys Gly Asn Phe Xaa Gln Leu Phe                425                 430                 435Lys Ser Ile Glu Asp Tyr Glu Lys Ser Leu Xaa Xaa Lys Xaa Ala                440 Ala Ala Ala Ala Thr Ala Gln Gly Ser;

-   -   wherein        -   Xaa at position 158 is Pro or Lys;        -   Xaa at position 182 is Leu or Met;        -   Xaa at position 189 is Asp or Pro;        -   Xaa at position 191 is Ala, Gly or Leu;        -   Xaa at position 205 is Ser or Thr;        -   Xaa at position 206 is Pro, Gln or Ser;        -   Xaa at position 211 is Tyr or Leu;        -   Xaa at position 214 is Ser, Asn or Thr;        -   Xaa at position 227 is Ala or Gly;        -   Xaa at position 340 is Arg or Lys;        -   Xaa at position 342 is Ala or Val;        -   Xaa at position 356 is Glu, Lys or Arg;        -   Xaa at position 360 is Met or Leu;        -   Xaa at position 366 is Gln or Glu;        -   Xaa at position 376 is Pro or Trp;        -   Xaa at position 385 is Leu, Ile or Val;        -   Xaa at position 387 is Ile or Leu;        -   Xaa at position 390 is Arg or Asn;        -   Xaa at position 417 is Gly, Gln or Ser;        -   Xaa at position 431 is Glu or Phe;        -   Xaa at position 432 is Ala, Arg or Lys;        -   Xaa at position 434 is Gln, His or Arg;    -   wherein one or more amino acid(s) designated by Xaa in SEQ ID        NO:82 is an amino acid different from the corresponding amino        acid of SEQ ID NO: 1; and wherein the polypeptide having        4-hydroxyphenylpyruvate dioxygenase activity has improved        insensitivity to an HPPD inhibitor compared to the polypeptide        of SEQ ID NO: 1.

4. A recombinant polypeptide having 4-hydroxyphenylpyruvate dioxygenase(HPPD) activity; wherein the polypeptide having 4-hydroxyphenylpyruvatedioxygenase activity comprises:

(SEQ ID NO: 83)                5                   10                  15Met Gly Pro Thr Pro Thr Ala Thr Ala Ala Gly Ala Ala Val Ala                20                  25                  30Ala Ala Ser Ala Ala Glu Gln Ala Ala Phe Arg Leu Val Gly His                35                  40                  45Arg Asn Phe Val Arg Phe Asn Pro Arg Ser Asp Arg Phe Gln Thr                50                  55                  60Leu Ala Phe His His Val Glu Leu Trp Cys Ala Asp Ala Ala Ser                65                  70                  75Ala Ala Gly Arg Phe Ser Phe Ala Leu Gly Val Pro Leu Ala Ala                80                  85                  90Arg Ser Asp Leu Ser Thr Gly Asn Ser Ala His Ala Ser Leu Leu                95                  100                 105Leu Arg Ser Gly Ser Leu Ser Leu Leu Phe Thr Ala Pro Tyr Ala                110                 115                 120His Gly Ala Asp Ala Ala Thr Ala Ala Leu Pro Ser Phe Ser Ala                125                 130                 135Ala Ala Ala Arg Arg Phe Ala Ala Asp His Gly Leu Ala Val Arg                140                 145                 150Ala Val Ala Leu Arg Val Ala Asp Ala Glu Asp Ala Phe Arg Ala                155                 160                 165Ser Val Ala Ala Gly Ala Arg Xaa Ala Phe Gly Pro Val Asp Leu                170                 175                 180Gly Arg Gly Phe Arg Leu Ala Glu Val Glu Leu Tyr Gly Asp Val                185                 190                 195Val Xaa Arg Tyr Val Ser Tyr Pro Asp Gly Xaa Ala Gly Glu Pro                200                 205                 210Phe Leu Pro Gly Phe Glu Gly Val Ala Ser Xaa Gly Ala Ala Asp                215                 220                 225Xaa Gly Leu Xaa Arg Phe Asp His Ile Val Gly Asn Val Pro Glu                230                 235                 240Leu Ala Pro Ala Ala Ala Tyr Xaa Ala Gly Phe Thr Gly Phe His                245                 250                 255Glu Phe Ala Glu Phe Thr Thr Glu Asp Val Gly Thr Thr Glu Ser                260                 265                 270Gly Leu Asn Ser Met Ala Leu Ala Asn Asn Ser Glu Asn Val Leu                275                 280                 285Leu Pro Leu Asn Glu Pro Val His Gly Thr Lys Arg Arg Ser Gln                290                 295                 300Ile Gln Thr Phe Leu Asp His His Gly Gly Pro Gly Val Gln His                305                 310                 315Ile Ala Leu Ala Ser Asp Asp Val Leu Arg Thr Leu Arg Glu Met                320                 325                 330Arg Ala Arg Ser Ala Met Gly Gly Phe Glu Phe Leu Pro Pro Pro                335                 340                 345Leu Ser Asp Tyr Tyr Asp Gly Val Arg Xaa Cys Ala Gly Asp Val                350                 355                 360Leu Thr Glu Ala Gln Ile Asn Glu Cys Gln Xaa Leu Gly Val Met                365                 370                 375Val Asp Arg Asp Asp Xaa Gly Val Leu Leu Gln Ile Phe Thr Lys                380                 385                 390Pro Val Gly Asp Arg Pro Thr Phe Phe Xaa Glu Xaa Ile Gln Arg                395                 400                 405Ile Gly Cys Xaa Glu Lys Asp Glu Lys Gly Gln Glu Tyr Gln Lys                410                 415                 420Gly Gly Cys Gly Gly Phe Gly Lys Gly Asn Phe Xaa Gln Leu Phe                425                 430                 435Lys Ser Ile Glu Asp Tyr Glu Xaa Ser Leu Glu Xaa Lys Xaa Ala                440 Ala Ala Ala Ala Thr Ala Gln Gly Ser;

-   -   wherein        -   Xaa at position 158 is Pro or Lys;        -   Xaa at position 182 is Leu or Met;        -   Xaa at position 191 is Ala or Gly;        -   Xaa at position 206 is Pro, Ser or Gln;        -   Xaa at position 211 is Tyr or Leu;        -   Xaa at position 214 is Ser or Asn;        -   Xaa at position 233 is Met or Val;        -   Xaa at position 340 is Arg or Lys;        -   Xaa at position 356 is Glu, Lys or Arg;        -   Xaa at position 366 is Gln or Glu;        -   Xaa at position 385 is Leu, Ile or Val;        -   Xaa at position 387 is Ile or Leu;        -   Xaa at position 394 is Met, Val or Lys;        -   Xaa at position 417 is Gly, Ser or Gln;        -   Xaa at position 428 is Lys or Arg;        -   Xaa at position 432 is Ala, Lys or Arg;        -   Xaa at position 434 is Gln, Arg or His;    -   wherein one or more amino acid(s) designated by Xaa in SEQ ID        NO:83 is an amino acid different from the corresponding amino        acid of SEQ ID NO: 1; and wherein the polypeptide having        4-hydroxyphenylpyruvate dioxygenase activity has improved        insensitivity to an HPPD inhibitor compared to the polypeptide        of SEQ ID NO: 1.

5. The polypeptide of embodiments 1-4, wherein the polypeptide furthercomprises substitution of one or more conservative amino acids,insertion of one or more amino acids, deletion of one or more aminoacids, and combinations thereof.

6. The polypeptide of any of embodiments 1-5, wherein the polypeptidehas an ON rate ratio of at least about 0.5; wherein the ON rate ratio isthe ratio of the reaction rate with herbicidal inhibitor to the reactionrate without herbicidal inhibitor; and wherein the reaction rates aredetermined in an in vitro assay.

7. The polypeptide of embodiment 6, wherein the herbicidal inhibitor ismesotrione or tembrione.

8. The polypeptide of embodiment 6 or 7, wherein in vitro assay iscarried out in the presence of 60 or 120 nM of the4-hydroxyphenylpyruvate dioxygenase protein.

9. The polypeptide of any of embodiments 6-8, wherein in vitro assay iscarried out in the presence of 100 μM 4-hydroxyphenylpyruvate.

10. The polypeptide of any of embodiments 6-9, wherein the polypeptidehas an OFF rate ratio of at least about 0.3; wherein the OFF rate ratiois the ratio of the steady state rate in the presence of inhibitor tothe initial reaction rate in the absence of inhibitor; and wherein thereaction rates are determined in an in vitro assay.

11. The polypeptide of embodiment 10, wherein the herbicidal inhibitoris mesotrione or tembrione.

12. The polypeptide of embodiment 10 or 11, wherein the in vitro assayis carried out in the presence of 60 or 120 nM of the4-hydroxyphenylpyruvate dioxygenase protein.

13. The polypeptide of any of embodiments 10-12, wherein the in vitroassay is carried out in the presence of 100 μM 4-hydroxyphenylpyruvate.

14. The polypeptide of any of embodiments 1-13, wherein the polypeptidehas a fitness parameter of about 2 to about 200 min⁻¹ μM⁻¹, and wherein

${{Fitness}\mspace{14mu}{Parameter}} = {\frac{k_{cat}}{K_{m}} \times {\left( {{ON}\mspace{14mu}{rate}\mspace{14mu}{ratio} \times {OFF}\mspace{14mu}{rate}\mspace{14mu}{ratio}} \right).}}$

15. A nucleic acid construct comprising a polynucleotide sequenceencoding a polypeptide having 4-hydroxyphenylpyruvate dioxygenase (HPPD)activity; wherein the polypeptide encoded is the polypeptide of any ofembodiments 1-14.

16. The nucleic acid construct of embodiment 15, further comprising apromoter operably linked to the polynucleotide sequence.

17. A plant cell comprising a nucleic acid construct comprising apolynucleotide sequence encoding a polypeptide having4-hydroxyphenylpyruvate dioxygenase (HPPD) activity; wherein thepolypeptide encoded is the polypeptide of any of embodiments 1-14.

18. The plant cell of embodiment 17, wherein the nucleic acid constructfurther comprises a promoter operably linked to the polynucleotidesequence.

19. The plant cell of embodiments 17 or 18, wherein the plant cellexhibits has an improved insensitivity to an HPPD inhibitor compared toa wild type plant cell of the same species, strain or cultivar.

20. The plant cell of any of embodiments 17-19, wherein the polypeptidehaving 4-hydroxyphenylpyruvate dioxygenase activity is present in anamount from about 1000 ppm to about 5000 ppm.

21. The plant cell of any of embodiments 17-19, wherein the polypeptidehaving 4-hydroxyphenylpyruvate dioxygenase activity is present in anamount from about 200 ppm to about 4000 ppm.

22. The plant cell of any of embodiments 17-21, wherein the nucleic acidconstruct is stably incorporated into the genome of the plant cell.

23. The plant cell of any of embodiments 17-22, wherein the plant cellis from a monocot.

24. The plant cell of embodiment 23, wherein the monocot is maize,wheat, rice, barley, sugarcane, sorghum, or rye.

25. The plant cell of any of embodiments 17-22, wherein the plant cellis from a dicot.

26. The plant cell of embodiment 24, wherein the dicot is soybean,Brassica, sunflower, cotton, or alfalfa.

27. The plant cell of any of embodiments 17-26, wherein the plant cellfurther comprises at least one additional polypeptide impartingtolerance to an additional herbicide.

28. The plant cell of embodiment 27, wherein the at least onepolypeptide imparting tolerance to an additional herbicide comprises:(a) a sulfonylurea-tolerant acetolactate synthase; (b) animidazolinone-tolerant acetolactate synthase; (c) a glyphosate-tolerant5-enolpyruvylshikimate-3-phosphate synthase; (d) a glyphosate-tolerantglyphosate oxido-reductase; (e) a glyphosate-N-acetyltransferase; (f) aphosphinothricin acetyl transferase; (g) a protoporphynrinogen oxidase.(h) an auxin enzyme; (i) a P450 polypeptide; or, (j) an acetyl coenzymeA carboxylase (ACCase).

29. The plant cell of embodiment 27, wherein the at least onepolypeptide imparting tolerance to an additional herbicide comprises ahigh resistance allele of acetolactate synthase (HRA) and/or aglyphosate-N-acetyltransferase polypeptide.

30. The plant cell of embodiment 27, wherein the plant cell furthercomprises at least one additional polypeptide imparting tolerance to anHPPD herbicide.

31. The plant cell of embodiment 30, wherein the at least one additionalpolypeptide imparting tolerance to an HPPD herbicide comprises a P450polypeptide or NSF1.

32. A plant comprising the plant cell of any of embodiments 17-31.

33. An explant comprising the plant cell of any of embodiments 17-31.

34. A transgenic seed produced by the plant of embodiment 32.

35. A method of producing a 4-hydroxyphenylpyruvate dioxygenase (HPPD)herbicide tolerant plant cell comprising transforming a plant cell witha polynucleotide encoding the polypeptide of any of embodiments 1-14 orthe nucleic acid construct of embodiments 15-16.

36. The method of embodiment 35, further comprising selecting a plantcell which is resistant to an HPPD herbicide by growing plant cells inthe presence of a concentration of an HPPD herbicide that bleaches theplant cell which does not comprise a polynucleotide encoding thepolypeptide of any of embodiments 1-14 or the nucleic acid construct ofembodiments 15-16.

37. The method of embodiment 36, wherein the method comprises

-   -   (a) culturing the plant cell in the presence of a sufficient        concentration of an HPPD herbicide such that the plant cells        display bleaching;    -   (b) transforming into the plant cells of step (a) a        polynucleotide encoding the polypeptide of any of embodiments        1-14 or the nucleic acid construct of embodiments 15-16; and    -   (c) growing the plant cells of (b), wherein transformed plants        cells no longer display bleaching.

38. The method of embodiment 35, wherein the method further comprisesregenerating a transgenic plant from the plant cell.

39. The method of embodiment 35, wherein the transforming the plant cellresults in the sTable 2ntegration of the polynucleotide into the genomeof the plant cell.

40. The method of embodiment 35, wherein the transforming the plant cellresults in the sTable 2ntegration of the polynucleotide into the genomeof a chloroplast in the plant cell.

41. A method for controlling weeds in a field containing a cropcomprising:

-   -   (a) planting the field with the transgenic seeds of embodiment        34; and,    -   (b) applying to any crop and weeds in the field a sufficient        amount of an HPPD herbicide to control weeds without        significantly affecting the crop.

42. The method of embodiment 41, wherein the HPPD herbicide comprises atleast one of triketones, isoxazoles, pyrazoles, or benzobicyclon oractive derivatives thereof or an agriculturally acceptable salt thereof.

43. The method of embodiment 42, wherein the HPPD herbicide comprises atleast one of mesotrione, sulcotrione, topremezone, and tembotrione,pyrasulfotole, isoxaflutole, benzofenap, pyrazoxyfen, or pyrazolynate oractive derivative thereof or an agriculturally acceptable salt thereof.

44. The method of embodiment 41, further comprising applying to the cropand weeds in the field a sufficient amount of at least one additionalherbicide comprising glyphosate, bialaphos, phosphinothricin,azafenidin, butafenacil, sulfosate, glufosinate, an ALS inhibitor, or aprotox inhibitor.

45. A method for detecting an HPPD polypeptide comprising analyzingplant tissues using an immunoassay comprising at least one antibody thatrecognizes the polypeptide of any of embodiments 1-14.

46. A method for detecting the presence of a polynucleotide encoding thepolypeptide of any of embodiments 1-14 comprising assaying plant tissueusing PCR amplification and detecting the polynucleotide.

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EXAMPLES Example 1. Experimental Methods

Immuno-Localization Electron Microscopy

Briefly, native or heterologously expressed HPPD was tagged withaffinity purified rabbit anti-HPPD antibodies, which were labeled withgoat anti-rabbit F(ab′) conjugated with μtltrasmall gold particles(Aurion, The Netherlands). Gold labeling was followed by silverenhancement (Aurion). Sections were counterstained with 4% uranylacetate (aqueous) followed by Reynold's lead citrate and examined byelectron microscopy.

Genomic and Transcript Analysis

A synthetic maize wild-type HPPD cDNA (NCBI Reference Sequence:NM_001112312.1) was assembled from commercially synthesizedoligonucleotides. During the synthesis of the gene, an NcoI restrictionsite was engineered into the start of the sequence to facilitatecloning. The change of codons (C)ATG CCC to (C)ATG GGT resulted in thesubstitution of glycine for proline at position 2. An EST(sgc5c.pk001.j9) coding for soybean HPPD was identified from aDuPont-Pioneer proprietary G. max EST database using conventionalbioinformatic tools including BLAST of the HPPD sequence described inCahoon and Coughlan (2007). The soybean HPPD coding region sequence wascloned from the EST cDNA into a T7-based bacterial expression vector.Expression, purification and characterization of the G. max HPPD proteinproved that the encoded protein was a functional HPPD, able to catalyzethe reaction from 4-hydroxyphenylpyruvate to homogentisate. Using thissoybean HPPD coding sequence as query, Pioneer Unigene PS0409914 wasidentified. Search of the genome assembly database with the unigene asquery resulted in identification of approximately 2 kb genomic sequenceupstream of the EST. To validate the genomic sequence, polymerase chainreaction (PCR) primers (forward primer: GCAAGTATTTCAATACAATAGC (SEQ IDNO:84) and reverse primer: GTTATCTGATATGATGTTGC (SEQ ID NO:85)) weredesigned and used to amplify the HPPD locus from genomic DNA isolatedfrom an elite soybean variety and the common Jack variety, followingprotocols for isolation of plant genomic DNA (Qiagen, Germantown, Md.).PCR reaction parameters were: Cycle1: 94° C., 2 min; Cycle 2 to 30: 94°C., 30 s; 65° C., 1 min; 72° C., 5 min; Cycle 31: 72° C., 10 min. Aproof-reading DNA polymerase, pfu Turbo (Stratagene, La Jolla, Calif.)was used for PCR amplification. A 4306 bp fragment and a 4310 bpfragment were obtained from elite and Jack, respectively. Thesefragments were cloned into Zero blunt TOPO PCR cloning vectors(Invitrogen, Carlsbad, Calif.) and fully sequenced. Each locus comprises3′ sequences, HPPD coding region, and upstream genomic sequence. Theloci are highly conserved, with an overall 99% sequence identity at thenucleotide level. A 462 bp intron and a 459 bp intron in the HPPD codingregion were identified in elite and Jack, respectively.

RNA ligation mediated 5′ rapid cloning of cDNA ends (5′ RACE) was usedto validate transcription start sites for the native HPPD promoter usingtotal RNA extracted from young soybean leaves and First Choice RLM-RACEkit (Ambion) per manufacturer's protocol. Total RNA was isolated withthe Qiagen RNeasy mini kit. Linked transcription-translation wasperformed in wheat germ extracts using 3′ truncated G. max HPPDtranscription vectors. Tissue specific patterns of expression for G. maxHPPD, EPSPS, ALS, and ACT2/7 genes were compiled from expression data inSoyBase (soybase.org) using the Soybean Breeder's Toolbox search.

Expression Vectors for Localization Microscopy

Vectors for transient expression in monocot species were constructed inwhich N-terminal fragments of monocot HPPD proteins or the soybean HPPDprotein and the synthetic monocot consensus peptide were fused to thegene coding for Discosoma sp. red fluorescence protein 2 (DsRed2;Clonetech, Mountain View Calif.) and inserted into a binary expressionvector under control of the maize rubisco activase promoter (Liu et al.,1996) or Arabidopsis Ubiquitin 10 promoter (Norris, et al., 1993) andterminated with the Solanum tuberosum proteinase inhibitor II (pinII)terminator region (An et al., 1989) with a hygromycin selectioncassette. The vector also contained an untargeted Zs Green cassette toprovide cytoplasmic contrast and a kanamycin selection cassette. Allthree genes were between left and right border sequences ofAgrobacterium T-DNA. A positive control vector was identical except thatthe insert was DsRed2 fused to the chloroplast targeting peptide ofArabidopsis rubisco activase, while a negative control was DsRed2 withno targeting sequence.

A second set of florescent vectors was made with N-terminal fragmentsencoding either the maize or soybean N-terminal HPPD protein fragmentsfused to a gene encoding Aequorea coerulescens green fluorescent protein1 (AcGFP1) and inserted into a binary expression vector under control ofthe Arabidopsis Ubiquitin 10 promoter (Norris et al., 1993) andterminated with the G. max Kunitz trypsin inhibitor 3 terminator region(NCBI accession S45092). Such vectors were used for either stable ortransient gene expression in plant cells. Fusions for testing thesoybean CTP function contained the sequence encoding amino acid residues1-42 or 1-86 of the long G. max HPPD protein. Another contained thesequence encoding residues 1-44 of the short HPPD protein (correspondingto residues 42-86 of the long protein). A positive control vector wasidentical except that the AcGFP1 coding region was fused to the 6H1synthetic chloroplast targeting peptide (Lassner and Wilkinson, 2008),while a negative control was AcGFP1 with no targeting sequence.

Promoter Constructs

Cassettes for testing transient expression of promoters were similar tothe DsRed N-terminal test vectors except that G. max HPPDpromoter-derived fragments replaced the rubisco and UBQ10 promoters. A2061 bp fragment comprising the native HPPD promoter of elite G. max wascreated from the upstream genomic sequence. The PCR reaction used(forward primer hp0234: GTTTTCCGCGGGTGTTGATCC (SEQ ID NO:86) and reverseprimer hp2296: TCATTGGTACCTGGTGTGGTGTGATGCTGC (SEQ ID NO:87)) introducedSacII and KpnI restriction sites. This fragment was isolated bygel-purification, digested with restriction enzymes SacII and KpnI, andligated to a DsRed2 marker gene to form the native G. max HPPD promoterexpression cassette. Introduction of the KpnI site between the promoterfragments and DsRed2 resulted in the introduction of a two amino acidlinker (GGTACC gly-thr) in the fusion proteins containing the longprotein CTP region.

The 1225 bp genomic sequence at the 3′ end of the promoter fragment wassubjected to in silico promoter analysis using Promoter REAPer andPromoter Delineator (Simmons and Navarro Acevedo, 2007). Genomicsequence from other species including Arabidopsis thaliana, Medicagotruncatula, Populus trichocarpa, Brassica rapa, Vitis vinifera, and themonocot Sorghum bicolor were included for comparison in this analysis.With the program Promoter REAPer, regions were identified in the soybeanHPPD promoter that are predicted to be important for its activity basedon the sequence conservation of a set of DNA motifs across the sevenplant species. To evaluate the predicted TATA boxes in promoteractivity, a deletion series was created with the 2061 bp template usingPCR with forward primer hp0234: GTTTTCCGCGGGTGTTGATCC (SEQ ID NO: 86)and the reverse primers as follows: SHP103C, hp2154:AGCATGGTACCTTGCGTCTGGGTTGAG (SEQ ID NO:88); SHP110C, hp2048:ATCTGGTACCTGATGTTGATGCGGC (SEQ ID NO:89); SHP000C, hp1962:AGGAGGTACCGTCAAATCCACCTAG (SEQ ID NO:90); SHP102C, hp1791:AGCCTGGTACCTTGTGTGTAAAAAAGATAAGAC (SEQ ID NO:91); and SHP101C, hp1663:TCCTTGGTACCTGATGCACTATATAACG (SEQ ID NO:92). Single or triple mutationsin the putative TATA boxes (see Table 4) were created usingsite-directed mutagenesis (Quick Change, Stratagene). Resultant deletionand mutated promoter fragments were fused with DsRed2 to createcassettes for analysis of expression activity in agro-infiltrated leaftissues.

SHP101C and SHP102C lack promoter activity due to deletion of activeTATA binding sites. To create synthetic promoters using thesenon-promoter DNA fragments, synthetic element I or II, each flanked byrestriction sites XhoI and KpnI, were synthesized and ligated with the3′ ends of the HPPD promoter-derived DNA fragments to create SHP101 and201 and SHP102 and 202, respectively. Synthetic element I comprises theSynII core (Bowen et al., 2000; sequence 1) sequence followed by the 45bp putative 5′UTR sequence including the predicted transcription startsite from the soybean native HPPD gene(ACAACCACCAAGCTCAATCTCAAGCAGCAGCATCACACCACACCA (SEQ ID NO:93),nucleotides between TATA3 and ATG). Synthetic element II contains theRsyn7 region (Bowen et al., 2000, sequence 2) immediately upstream ofsynthetic element I. In a similar manner, promoters SHP103, 104, 105,106, 107, 108, and 109 were created with element I and SHP203, 204, 205,206, 207, 208, and 209 were created with synthetic element II. InSHP110, a partial SynII core sequence is inserted in place of TATA5. InSHP210, TATA5 through transcription start site at −237 is deleted andreplaced with Rsyn7 plus the partial SynII core sequence. SHP110e is thesame as SHP110 with the addition of a CaMV enhancer (Ow et al., 1987) atthe 5′ end of the promoter fragment. In SHP111, the sequenceencompassing TATA3 through transcription start site at +1 is deleted andreplaced with the partial SynII core sequence. In SHP120C an A to Tmutation eliminates the start codon of the upORF element.

Agrobacterium-Infiltration and Florescence Measurements

All seedling plants were grown in growth chambers with 16 hr light at375-450 μm m⁻² s⁻¹, 26° C. day and 22° C. night. Expression plasmids forlocalization studies were transformed into Agrobacterium tumefaciensAGL-1 via electroporation according to Shen and Forde (1989) andagro-infiltration (Kapila et. al., 1997) used to introduce theconstructs into plant cells. Agrobacterium cultures were grown overnightin LB with 40 mg/L kanamycin and a working suspension normalized to 1.0OD₆₀₀ in 10 mM MgSO₄, 400 μm acetosyringone and 1 mM DTT. Leaves of3-week old maize or sorghum seedlings were infiltrated with theAgrobacterium, and examined by fluorescence microscopy two days later(Nikon Eclipse 80i, DsRed2 filter set). Infiltrated leaf samples werederived from plants of uniform developmental stage grown under the sameconditions. Leaves of 4-week old Nicotiana benthamiana, 8-day oldPhaseolus vulgaris, (variety Shade) and 10-day old Glycine max seedlingswere infiltrated with the Agrobacterium, and examined by fluorescencemicroscopy 4 and 5 days later.

Agrobacterium strains expressing plasmids for promoter characterizationwere infiltrated into bush bean leaf tissues. Visual analysis confirmedthat the native G. max HPPD promoter DNA fragment was able to drive theexpression of DsRed2 in infiltrated leaf tissues compared withfluorescent background from leaf tissues infiltrated with a negativecontrol construct consisting of the dMMV promoter (Dey and Maiti, 1999)driving a beta-glucuronidase reporter. Relative promoter strength wasdetermined by quantitative measurement of the red fluorescence generatedfrom expressed DsRed2 protein in infiltrated leaf tissues. Redfluorescence from 50 μg of protein extracted from infiltrated leaf discswas quantified using a Typhoon Trio+ Variable Mode Imager. Infiltrationexperiments for each construct were repeated at least three times. Thebackground red fluorescence detected in leaves infiltrated with thenegative control vector was subtracted for data normalization. TheDsRed2 readouts were used to calculate the level of DsRed2 from eachconstruct relative to the DsRed2 expressed from the full native promoterconstruct (2061 nucleotides 5′ to the ATG of the short protein), whichwas set to 100%. Up to 30 leaf discs infected with the same culture werepooled for analysis. Each pool of infiltrated leaf samples represented(about 260 mg fresh weight) tissue equally derived from 15 plants ofuniform developmental stage.

Qualitative assessment of promoter strength was determined 4-5 dayspost-infection by visually inspecting treated samples under a stereofluorescent microscope (Leica Microsystems—Wetzlar, Germany; M165 FCwith DsRed2 Filter set; Ser. No. 10/447,412), and acquiring images(Leica Microsystems—Wetzlar, Germany; DFC300 FX R2) of representativeexamples at fixed exposure time of 7 seconds.

HPPD Expression and Purification

A synthetic maize wild-type HPPD gene (referred to herein as the maizewild-type sequence) was assembled from commercially synthesizedoligonucleotides to deliver the amino acid sequence of SEQ ID NO: 1.During the synthesis of the gene, an NcoI restriction site wasengineered into the start of the sequence to facilitate cloning. Thechange of codons (C)ATG CCC to (C)ATG GGT resulted in the substitutionof Glycine for Proline at position 2 in SEQ ID NO:1 compared to themaize wild-type protein of WO 1997049816 SEQ ID NO: 11.

Wild type and shuffled variant genes were cloned into pVER7062, amodified version of pET24a(+)(Novagen), which places six histidineresidues at the N-terminus of the expressed protein. Vectors wereelectroporated into E. coli host strain BL21(DE3). Cells were grown at30 C in rich medium such as 2×YT containing the selection antibiotic,kanamycin. At a density of about 0.6 OD600, IPTG was added to 0.2 mM,the temperature was reduced to 16 C and growth continued for another 24hrs. Cells were harvested by centrifugation and stored at −80 C. Cellpellets were lysed in BPER (Pierce) protein extraction reagentcontaining 0.2 mg/ml lysozyme, 1 mM dithiothreitol, protease inhibitorcocktail (Sigma, bacterial cocktail) and endonuclease. Insolublecellular debris was removed by centrifugation. HPPD protein was purifiedfrom the soluble protein solution by affinity chromatography on thenickel form of nitrilotriacetic acid (Ni-NTA) resin (Qiagen). Proteinconcentrations were determined by the Bradford method, as supplied byBio-Rad.

Medium Browning Assay

The homogentisate produced by the HPPD reaction is not furthermetabolised by E. coli, but is converted to a brown ochronotic pigment(Zannoni V G et al., Biochimica Et Biophysica Acta 177: 94-105, 1969)Therefore, E. coli cells expressing active shuffled maize HPPD enzymeturn the medium brown, which constituted a convenient first tier screen.The screen was made more informative by including an HPPD inhibitor inthe medium, requiring that the HPPD variant be desensitized toinhibition as well as active. The intensity of browning was quantifiedby measuring absorbance at 360 nm. Those wells with absorbance greaterthat the appropriate standard were advanced to more refined screensinvolving in vitro enzyme assay.

HPPD Activity Assay

HPPD catalyzes the conversion of 4-hydroxyphenylpyruvate (HPP) tohomogentisate (FIG. 17). Substrate and product do not differ inabsorbance of light at any useful wavelength. However, the product ofthe ensuing reaction in tyrosine metabolism, maleylacetoacetate, absorbsstrongly at 320 nm. Furthermore, the enzyme catalyzing that reaction isalso a dioxygenase having similar mechanism and buffer requirements asHPPD, making homogentisate dioxygenase (HGD) an ideal partner in acoupled assay, as shown.

The HDG gene from Pseudomonas aeruginosa (Amaya (2004) Arch BiochemBiophys 421, 135-142) was cloned into pVER7062 and electroporated intoE. coli strain BL21(DE3). The enzyme was produced by methods similar tothose described for HPPD. The purified enzyme has a KM for homogentisateof 23 μM and a k_(cat) of 100/sec, properties highly suited forinstantly converting the homogentisate produced by HPPD tomaleylacetoacetate.

HPPD activity was measured by placing an aliquot (e.g., 6 μl) of thesubstrate HPP at 50-fold the desired final concentration into the wellsof a low UV-absorbing assay plate. Reactions were started by adding amixture (e.g., 294 μl) containing 25 mM Hepes, pH 7, 2 mM ascorbate, 10μM FeSO4, 1 to 100 μM HPP, 50 nM HGD and 5 to 240 nM HPPD. Absorbance at320 nm was monitored continuously in a plate-reading spectrophotometer(Spectramax, Molecular Devices).

HPPD Kinetic Parameters

The catalytic performance of wild-type HPPD and variants generated byshuffling was assessed by determining the substrate saturation kineticparameters. The Michaelis-Menten kinetics protocol of the Spectramaxsoftware was customized for HPP concentrations ranging from 3.33 μM to100 μM. Reaction rates were measured as described above for eachconcentration of HPP. The software returns values of K_(M) and Vmaxusing the Lineweaver-Burke transformation of the Michaelis-Mentenequation.

HPPD Inhibitor Sensitivity Parameters

The major HPPD inhibitors used in agriculture today are mesotrione,isoxaflutole, tembotrione, and topramezone. As seen in FIG. 1, thestructures share an aromatic ring and a pair of keto oxygens in commonwith the substrate 4-hydroxyphenylpyruvate, for which they arecompetitive inhibitors (Secor, 1994). The elements in which theinhibitors differ from the substrates (e.g., cyclohexane ring,substituents on the aromatic ring) present the opportunity to use geneshuffling to enable the enzyme to discriminate between the desired andundesired ligands. All herbicidal inhibitors of HPPD form a tightcomplex with the enzyme by the dual mechanisms of coordination to theactive site iron atom through a pair of keto oxygens and a pi stack ofthe aromatic ring of the inhibitor between a pair of active sitephenylalanines (Neidig et al., 2005). As a result, conventional I₅₀determinations are not able to distinguish differences in bindingaffinity among various forms of HPPD and the inhibitor. All values willsimilarly approximate 50% of the enzyme concentration.

To devise a parameter for detecting changes in inhibitor bindingaffinity, K_(D), one can utilize the relationship between K_(D) and therates of binding and release of inhibitor to and from the enzyme.

${E + I}\overset{k_{ON}}{\underset{k_{OFF}}{\rightleftarrows}}{EI}$At equilibrium, rates of binding and release are equal. Thus,k _(ON)[E][I]=k _(OFF)[EI]Written as a dissociation (products over reactants), the equation can bere-arranged to:

$\frac{\lbrack E\rbrack\lbrack I\rbrack}{\lbrack{EI}\rbrack} = {\frac{k_{OFF}}{k_{ON}} = K_{D}}$

Higher K_(D) (reduced affinity or increased insensitivity) can beattained with a numerically smaller ON rate, a larger OFF rate or both.To detect and quantify changes in k_(ON) and k_(OFF), observations ofthe time course of an HPPD reaction as inhibitor binds to andinactivates the enzyme (k_(ON)), or is released from a pre-formedenzyme-inhibitor complex (k_(OFF)) were used, as shown in FIGS. 13A and13B. In practice, a quantitative indicator of k_(ON) was obtained bymonitoring the time courses of HPPD reactions containing 60 or 120 nMHPPD and 100 μM HPP in the presence and absence of 4 μM inhibitor (e.g.,mesotrione or tembotrione). The ratio of the reaction rate withinhibitor to that without inhibitor during the 70 to 90 second intervalof the reaction was termed the “ON rate ratio”. The smaller the actualk_(ON), the more slowly the HPPD reaction decelerates and the higher thevalue is for the ON rate ratio. FIGS. 13A and 13B illustrate thecontrasting reaction velocity in the 70-90 sec interval for maizewild-type HPPD (FIG. 13A) versus an improved variant (SEQ ID NO:78)(FIG. 13B).

A quantitative indicator of k_(OFF) can be obtained by observing thetime course of an HPPD reaction as inhibitor is released from apre-formed enzyme-inhibitor complex. HPPD and inhibitor were incubatedtogether at concentrations of 7.2 and 8 μM, respectively. Incubationswith the same concentrations of enzyme but no inhibitor were done inparallel. After 1 hr at room temperature, 5 to 10 μl of theenzyme-inhibitor complex was dispensed into the wells of the assayplate. Reactions were started with the addition of 290 to 295 μl of 25mM Hepes, pH 7, 2 mM ascorbate, 10 μM FeSO₄, 100 μM HPP and 50 nM HGD.The reactions were monitored at 320 nm for 12 min. Reaction velocityaccelerates as inhibitor is released from the enzyme until a steadystate is reached, during which the reaction velocity is constant. Theratio of the steady state rate in mixtures containing herbicidalinhibitor to the initial velocity of mixtures lacking inhibitor istermed the “OFF rate ratio”.

Another parameter to record is the time span required for the reactionswith inhibitor to reach the steady state. FIGS. 13C and 13D illustratethe contrasting time span in which maize wild-type HPPD (FIG. 13C) andan improved variant (SEQ ID NO:78) (FIG. 13D) dissociated frommesotrione, as indicated by the accelerating reaction rates. The plateauof absorbance is due to exhaustion of the substrate. With the improvedvariant, not only was the steady state attained in a shorter time span(80 sec for the variant versus 280 sec for wild type), the velocityattained was twice as high as with wild type, though the enzymes werepresent at the same concentration (240 nM). This is because a largerfraction of the variant enzyme is free of inhibitor compared to thewild-type enzyme, and the k_(cat) for both is nearly the same, about 220min⁻¹.

It is not certain that the steady state attained in the OFF ratereactions actually represents an equilibrium where OFF rates are nowequal to ON rates. Because substrate and inhibitors bind in the samesite, the high concentration of substrate present may competitively trapthe inhibitor and prevent it from binding again. To be sure thatimprovement in ON rates is being taken into account, the ON and OFF rateratios were multiplied, creating an “insensitivity parameter” that is asurrogate for K_(D). K_(D) is expressed as k_(OFF)/k_(ON), but becausethe ON rate ratio is an inverse parameter (the higher the value of ONrate ratio, the lower the value of the represented phenomenon, k_(ON)),it is appropriate to multiply ON and OFF rate ratios rather then divideOFF rate ratio by ON rate ratio. Another parameter, which quantifies thecombined catalytic and insensitivity properties of the enzyme isk_(cat)/K_(M)×ON rate ratio×OFF rate ratio, and is termed “traitfitness”. This parameter is intended to have a meaning similar to thecommonly used expression k_(cat)/K_(M)×K_(i).

The diketonitrile form of isoxaflutole was synthesized by DuPontchemists. All other inhibitors were obtained from Sigma-Aldrich. Thecompounds shown in FIG. 16 can be synthesized by previously describedmethods known to one skilled in the art.

HPPD Protein Detection in Planta

HPPD protein concentration in young soybean leaves was measured usingLC-MS/MS (liquid chromatography coupled with tandem mass spectrometry)according Hu and Owens (2011) with some modifications. 600 μL of PBSTbuffer were added to extract 10 leaf punches after being lyophilized andground with Spex Certiprep 2000 GenoGrinder. The total extractedproteins (TEP) were measured with Bradford assay and all the sampleswere normalized to 0.8 μg/μL TEP. 50 μL normalized transgenic extractswere used for analysis and different amount of protein standards werespiked into 50 μL of negative tissue extracts to prepare standardcurves. All samples were then heated for 15 min at 95° C. oven and 80 μLdigestion buffer ABCT (100 mM ammonium bicarbonate with 0.05% Tween-20)was added. The samples were reduced with 6 μL of 0.25 M dithiothreitolat 50° C. for 30 min and then were alkylated with 6 μL of 0.3 Miodoacetamide at room temperature in the dark for 30 min. 1 μg oftrypsin (in 10 μL) was added to each sample and digestion lasted about18 hours before 10 μL 10% (v/v) formic acid and 10 μL internal standard(peptide SIEDYEK where K was labeled with sTable 2sotopes ¹³C and ¹⁵N)were added. HPPD protein was quantified by its signature tryptic peptideSIEDYEK using Waters UPLC coupled with AB SCIEX QTRAP 4000 or 5500.Autosampler temperature was kept at 5° C. during analysis. 10 μL wereinjected onto an Aquasil 100×2.1 mm 3μ C18 column (ThermoFisher) kept at60° C. Mobile phases consisted of 0.1% formic acid (MPA) and 0.1% formicacid in acetonitrile (MPB), and LC was performed at a flow rate of 0.6mL/min with linear gradient of 5-16% MPB in 2.5 min. The MRM transitionsof 442.3/683.3 and 446.3/691.3 were monitored for peptide SIEDYEK andits internal standard peptide, respectively. Chromatogram peak arearatios to the corresponding IS were plotted against proteinconcentrations. The limit of quantifiable detection of HPPD by mass specanalysis is about 0.003% of total extractable protein (30 ppm, Hu andOwens, 2011)

Stable Soybean Transformation

Soybean plants expressing HPPD variant transgenes were produced usingthe method of particle gun bombardment (Klein et al., 1987) using aDuPont Biolistic PDS1000/He instrument. A selectable marker used tofacilitate soybean transformation was a chimeric gene composed of theS-adenosylmethionine synthase (SAMS) promoter (Falco and Li, 2010) fromsoybean, a highly resistant allele of soybean acetolactate synthase(Bedbrook et al., 1997), and the native soybean acetolactate synthaseterminator region. The selection agent used during the transformationprocess was chlorsulfuron. HPPD genes were expressed with a syntheticconstitutive promoter (Bowen et al., 2000) or the G. max HPPD derivedpromoters, an insensitive HPPD variant, and an Arabidopsis ubiquitin3gene terminator (Callis et al., 1995). Bombardments were carried outwith linear DNA fragments purified away from any bacterial vector DNA.The selectable marker gene cassette was in the same DNA fragment as theHPPD cassette. In some cases the characterized CTP sequences 6H1(Wilkinson and Lassner, 2008) and the Arabidopsis rubisco large subunitCTP (Lee et al., 2006) were fused to a truncated maize HPPD variant.Bombarded soybean embryogenic suspension tissue was cultured for oneweek in the absence of selection agent, then placed in liquid selectionmedium for 6 weeks. Putative transgenic suspension tissue was sampledfor PCR analysis to determine the presence of the HPPD gene. Putativetransgenic suspension culture tissue was maintained in selection mediumfor 3 weeks to obtain enough tissue for plant regeneration. Suspensiontissue was matured for 4 weeks using standard procedures; maturedsomatic embryos were desiccated for 4-7 days and then placed ongermination induction medium for 2-4 weeks. Germinated plantlets weretransferred to soil in cell pack trays for 3 weeks for acclimatization.Plantlets were potted to 10-inch pots in the greenhouse for evaluationof herbicide resistance.

Herbicide Tolerance Testing

T0 plants with HPPD transgenes were grown to the V2 to V8 growth stageand then sprayed with commercial mesotrione formulation at rate 210 gai/ha (two times the labeled rate for corn in the field). All mesotrionetreatments were applied with 0.25% nonionic surfactant and 1% ammoniumsulfate in a spray volume of 374 L/ha. Individual plants were comparedto untreated plants of similar genetic background, evaluated forherbicide response at eight days after treatment and assigned a visualresponse rating from 0 (no effect) to 100 (dead plant). Sibling plantswere similarly evaluated with tembotrione at 93 g ai/ha. Proteinexpression level was determined by mass spectrometry (Hu and Owens,2011). In the T0 generation, plants that had improved tolerance comparedto controls based upon low injury scores (≤30%) were advanced to the T1generation for more extensive herbicide testing. When sibling clones ofthe events were available, the same process was carried out on T0 plantsusing tembotrione.

T1 plants were evaluated for zygosity. Homozygous single-locustransgenic plants and their corresponding null segregants wereidentified and T2 true breeding seed was obtained from each. Plants weregrown to the V1 to V2 growth stage and then sprayed with the commercialformulation of mesotrione at 420 g ai/ha. All treatments were appliedwith nonionic surfactant and ammonium sulfate in a spray volume of 374L/ha. Ratings of response to the herbicide were made eight days aftertreatment, as described for T0 plants.

Homozygous T3 generation seeds were planted in short rows in Johnston,Iowa at a DuPont Pioneer regulated field location. Herbicides wereapplied at the V4 stage with a backpack sprayer in a spray volume of 140L/ha at two or four times the labeled rates for corn in the field, whichare: mesotrione, 118 g ai/ha; tembotrione, 90 g ai/ha; isoxaflutole, 67g ai/ha. All treatments included 0.25% v/v nonionic surfactant and 8lb/100 gal ammonium sulfate. As negative controls, rows ofnon-transformed plants of the same variety were sprayed at the samerates. Positive control rows received no spray. Visual injury was ratedat 3, 7, and 14 days after treatment (DAT).

Example 2. Bioinformatic and Functional Localization Analysis of Z. mays(Maize) HPPD

A single HPPD gene was identified in Z. mays via genomic and ESTdatabase searches (NCBI Reference Sequence: NM_001112312.1) giving riseto a 444 amino acid encoded protein (FIG. 3A). ProtComp 6.1(linux1.softberry.com/berry.phtml) indicated a cytosolic location ofmaize HPPD (cytoplasmic score=14470; chloroplastic score=1.4).Similarly, WoLF PSORT (Horton et al., 2007) and TargetP (Emanuelsson etal., 2000) predict a cytosolic location of the HPPD protein. PCLR(Schein et al., 2001) predicts non-chloroplast localization with eitherthe N-terminal 55 residues or the whole protein (0.25 with 0.42threshold), Protein Prowler (Hawkins and Boden, 2006) predicts either amitochondrial (0.34) or chloroplast (0.39) location and Multiloc(Hoglund et. al., 2006) predicts an extracellular (0.74) localizationwith the first 50 amino acids of maize HPPD, but a strong chloroplastlocalization (0.97) for the full maize HPPD sequence.

Immuno-localization electron microscopy of maize tissue sections wascarried out to detect native HPPD localization. Gold labeling wasobserved mainly in bundle sheath chloroplasts (range; 5-28 particles perchloroplast, 50 chloroplasts observed (FIG. 10). Particles were alsofound in mesophyll chloroplasts, but in no other structures.Observations with direct detection of HPPD in maize tissues by labeling,protein purification using antibody pull-down, and mass-spectrometricprotein detection all indicated that HPPD accumulation in maize leavesis very low.

To functionally corroborate the localization of maize HPPD, a binaryplant transformation vector was constructed in which the portion of themaize HPPD gene coding for the N-terminal 50 amino acids was fused tothe gene coding for DsRed2 all under control of the maize rubiscoactivase promoter. A positive control vector was identical except thatthe DsRed2 insert was fused to the chloroplast targeting peptide (CTP)of maize rubisco activase, while a negative control was DsRed2 with notargeting sequence. The plasmids were transformed into Agrobacteriumtumefaciens AGL-1 and agrobacterium-infiltration was used to introducethe constructs into plant cells for transient expression.Agrobacterium-infiltration is a well described method (Kapila et. al.,1997) of introducing an Agrobacterium cell suspension to plant cells ofintact tissues so that reproducible infection and subsequent plantderived transgene expression may be measured or studied. Leaves of3-week old maize seedlings were infiltrated with the Agrobacterium, andexamined by fluorescence microscopy of hand sections two days later.With the vector where DsRed2 was fused to rubisco activase CTP, redfluorescence was seen in discrete packets in a pattern resemblingperi-nuclear chloroplasts, as expected (FIG. 3B). A similar pattern wasseen when DsRed2 was fused to the N-terminal 50 amino acids of maizeHPPD (FIG. 3C). Without targeting, fluorescence was diffuse with someconcentration in the nucleus (FIG. 3D). In another experiment confirmingthese results, maize leaf tissue was co-bombarded with DNA from both theDsRed2-containing test plasmids and a plasmid encoding untargeted cycle3 green fluorescence protein (C3GFP). Transformation of guard cells withvectors encoding either rubisco activase CTP-DsRed2 or the N-terminal 50amino acids of maize HPPD fused to DsRed2 clearly resulted in plastidtargeting of the DsRed2 reporter, whereas untargeted C3CFP showed nooverlap with the DsRed2 signal (FIG. 11).

To determine the length of the functional CTP for maize HPPD, vectorswere constructed in which the portion of the maize HPPD gene coding forthe N-terminal 0, 10, 20, 30, 40 or 50 amino acids was fused to the genecoding for DsRed2 and evaluated with transient expression followingagro-infiltration of maize leaves. Microscopy revealed that 50 aminoacids of the maize HPPD N-terminus effectively targeted DsRed2 toplastids (FIG. 3G), but 40 amino acids or fewer failed to do so, withDsRed2 fluorescence visible only in the cytoplasm (FIGS. 3E and 3F).This result indicates that more than 40 amino acids of the N-terminusare required for chloroplast localization and that 50 amino acids aresufficient for targeting.

To investigate if the maize HPPD protein is unique, several monocotsequences were compared. FIG. 3J provides an N-terminal alignment ofmonocot HPPD proteins having identities of 59-85%. A vector constructedin which the Oryza sativa HPPD N-terminal sequence was fused to the genecoding for DsRed2 was assayed in maize leaves as described. Microscopyrevealed that the 53 amino acid rice N-terminal sequence effectivelytargeted DsRed2 to maize plastids. In view of the conservation among thesequence of the monocot HPPD proteins, a consensus monocot HPPDchloroplast targeting peptide sequences was determined. The consensussequence, MPPTPTTAAATGAGAAAAVTPEHAAFRLVGHRRFVRFNPRSDRFHTLAFHHVE (SEQ IDNO:94), targeted the DsRed2 protein to the maize chloroplasts. Tofurther confirm the monocot functional similarity, the vectors targetingDsRed2 with 0, 10, 20, 30, 40, and 50 amino acids of the maize HPPDN-terminus were tested by agro-infiltration in sorghum (Sorghum bicolor)leaves. The results matched those obtained in maize. The data indicatethat the monocot HPPD proteins share a homologous chloroplast targetingmotif and function.

The function of the monocot HPPD sequence in dicots was explored bytransient expression in bush bean (Phaseolus vulgaris), tobacco(Nicotiana benthamiana), and soybean cells. The sequence encoding aminoacids 1-50 of the maize HPPD protein was fused to a gene encoding AcGFP1and inserted into a binary expression vector under control of theArabidopsis Ubiquitin 10 promoter. A positive control vector wasidentical except that the AcGFP1 coding region was fused to the 6H1synthetic chloroplast targeting peptide (Lassner and Wilkinson, 2008),while a negative control was AcGFP1 with no targeting sequence. Thefirst 50 amino acids of maize HPPD were sufficient to drive chloroplastimport of AcGFP1 in epidermal cells of P. vulgaris, although some greenfluorescence remained in the cytoplasm. In N. benthamiana the AcGFP1remained in the cytoplasm with none apparent in the chloroplasts.Results by bombardment in soybean showed AcGFP1 in both plastids andcytoplasm (FIG. 3H). This shows that the maize HPPD CTP is recognized indicot plant cells, but may be inefficiently processed. Stablytransformed soybean plants expressing the 50 amino acid N-terminal CTPfused to AcGFP1 showed strong fluorescence in the chloroplasts (FIG.3I), indicating that the inefficient translocation can be due to thehigh template concentration that occurs in transient expressionconditions.

Example 3. Bioinformatic and Functional Localization Analysis of G. max(Soybean) HPPD

G. max is a polyploid derived from 2 evolutionary genome duplications(Schmutz et al, 2010) and as such appears to have multiple paralogousHPPD genes. As some of the annotated genes appear incomplete or haverare ESTs, glyma14g03410.1 on chromosome 14 was studied. This soybeanHPPD protein has been previously annotated as a 449 amino acid proteinwith N-terminal sequence MPIPMCNEIQ (Cahoon and Coughlin, 2007; sequence36) and as a 443 amino acid protein with N-terminal sequence MCNEIQAQAQ(Genbank ABQ96868). Analysis of genomic and EST data revealed that anin-frame N-terminal extension of the previously annotated coding regionexists, adding 41 amino acids to produce a 490 amino acid full-lengthHPPD protein as shown in FIG. 4A. Furthermore, EST data reveal two majormRNAs, one of which is able to support translation of the 490 amino acidprotein and a smaller EST that is able to support translation of the 449amino acid protein.

5′ cap-dependent rapid cloning of cDNA ends (5′ RACE) revealed two majortranscripts for the native soybean HPPD gene. Cloning and sequencing ofthese PCR products revealed a shorter transcript that was designated asstarting at position +1. The longer transcript began at position −237relative to the shorter transcription start site (FIG. 4A). Sequence ofmultiple clones for each 5′ RACE product indicated an approximately 4nucleotide variation between individual transcripts for both sites.Linked in vitro transcription and translation indicated that both mRNAsare translated and make the predicted size protein (truncated forconvenience, FIG. 4B). The +1 transcript is translated to produce asingle protein, designated the “short” protein. The −237 transcriptyields two proteins, with the lower molecular weight band at the same MWas the single protein produced from the +1 transcript, indicating thattranslation can initiate at both positions on the long transcript. Thehigher MW protein produced from the −237 transcript is designated the“long” protein.

Bioinformatic evaluation of the shorter soybean HPPD sequence did notpredict a chloroplast or other targeting sequence. However, achloroplast targeting function was predicted for the N-terminallyextended form by ProtComp 9.0 (linux1.softberry.com), WoLF PSORT (Hortonet al., 2007) and PCLR (Schein et al., 2001). TargetP (Emanuelsson etal., 2000) indicates chloroplast localization, but gave a higher scoreto ‘other’ while MultiLoc2 (Blum et al., 2009) predicted a cytoplasmiclocalization for both the first 42 and the first 86 amino acids of thelong protein. Functional analysis was required to clarify thepredictions.

Transient expression experiments indicated that the long HPPD protein isimported to chloroplasts, while the short protein remains in thecytosol. Plant expression cassettes were constructed fusing portions ofthe N-terminus of the soybean HPPD to either DsRed2 or AcGFP1. The firstfusion contained amino acid residues 1-42 of the long protein while thesecond fusion contained residues 1-44 of the short HPPD protein(corresponding to residues 42-86 of the long protein). The third fusioncontained the full 1-86 amino acids of the long HPPD protein. Thesecassettes, under control of the Arabidopsis Ubiquitin 10 promoter, wereused to infect soybean seedling leaves. As shown in FIG. 4C-E,fluorescence is clearly visible in the chloroplasts of infected cellsonly when the marker gene is fused to amino acid residues 1-86. When thefusion is made with the shorter sequences of both proteins, fluorescenceis visible only in the cytoplasm. The pattern of dual localization seenwith the reporter constructs was confirmed by immuno-localizationelectron microscopy (FIGS. 12A and 12B). Thus, the N-terminal 42 aminoacids of the long protein is predicted to be a CTP, but to befunctional, a longer sequence is required.

Although the N-terminal sequences of maize and soybean HPPD differconsiderably (FIG. 4F), they are both able to target proteins in theheterologous species. Leaves of 4-week old maize seedlings wereinfiltrated with the Agrobacterium carrying the soybean constructs andexamined by fluorescence microscopy. Transient expression indicated thatthe long HPPD protein N-terminus did target the marker protein to maizecell chloroplasts, while the protein variant with the shorter N-terminusdelivered the protein to the cytosol. Thus, the dicot chloroplasttargeting region of soybean HPPD is able to function in monocot cells.

Because the reported HPPD sequences were mis-annotated for soybean,available sequence data for Arabidopsis and another legume, Medicagotrunculata (alfalfa), were examined to determine if other related dicotspecies showed the same N-terminal extension. The Arabidopsis chromosome1 HPPD gene NC_003070.9 (Genbank) encodes a 418 amino acid open readingframe with no upstream open reading frames extending the HPPD protein.The lack of N-terminal extension is punctuated by two in-frame stopcodons 15 nucleotides upstream of the ATG start. On the other hand, asearch of the M. trunculata genome returned a predicted HPPD genelocated on chromosome 5 (NC_016411.1; Genbank). The annotated predictedprotein of 437 amino acids is preceded by a long open reading frame thatcould initiate at methionines adding 74 or 115 amino acids. The 74N-terminal extension showed a very strong chloroplast localization scorewith PCLR (Schein et al., 2001) while the 115 amino acid extension didnot.

Example 4. Directed Evolution of the Maize HPPD Protein for IncreasedInsensitivity to Herbicide Inhibitors

Directed evolution is an iterative process whereby beneficial diversityis discovered and iteratively recombined to evolve variants that achievea desired protein engineering goal. A goal was to create an HPPD enzymethat retained kinetic activity yet was insensitive to most or allHPPD-inhibiting herbicides. Characterization of the maize and soybeanHPPD proteins showed that the former was 40-fold less sensitive tomesotrione than the latter (see Table 2 below, which shows kineticparameters of E. coli purified proteins of wild-type HPPD enzymes frommaize and soybean). Inhibition measurements are for the herbicidalcompound mesotrione. The maize enzyme was, therefore, chosen for use insoybean plants. Final evaluation of shuffled HPPD enzymes was carriedout with multiple HPPD herbicides to select the most robust variant.

TABLE 2 Insensitivity parameters Fitness SEQ Kinetic parameters ON OFFFold HPPD ID k_(cat), K_(M), rate rate ON x Fold ONxOFF vs Zm VariantNO. min⁻¹ (μM) k_(cat)/K_(M) ratio ratio OFF vs wt x k_(cat)/K_(M) wt Z.mays wt 1 219 6.4 34.2 0.20 0.31 0.06 2.10 1 G. max wt — 100 3.0 33.30.20 0.007 0.0014 0.023 0.047 0.02 R1 Exemplar — 86 4.0 21.6 0.44 0.120.05 0.9 1.2 0.6 R2 Exemplar — 50 2.7 18.9 0.70 0.18 0.13 2.1 2.4 1.1 R3Exemplar — 95.6 2.6 36.8 0.58 0.13 0.08 1.3 2.9 1.4 R4 Exemplar — 1174.3 27.5 0.61 0.16 0.10 1.6 2.7 1.3 R5-9043 — 146 5.9 24.7 0.60 0.630.38 6.2 9.3 4.4 R6-9075 79  114 4.0 28.9 0.68 0.68 0.46 7.6 13.4 6.4R7-9070 2 88.9 2.9 30.7 0.67 0.83 0.56 9.11 16.6 7.9 R8-1973 8 70.8 2.035.2 0.73 1.00 0.73 11.9 25.5 12.2

In the first 6 rounds, shuffled gene variant libraries were made basedon the maize HPPD protein template using techniques including familyshuffling, single-gene shuffling, back-crossing, semi-synthetic andsynthetic shuffling (Zhang J-H et al., 1997; Crameri et al., 1998; Nesset al., 2002). The amino acid diversity for those libraries originatedfrom phylogenetic sequence diversity, random mutagenesis, site-directedmutagenesis, and structural features based on crystal structures ofproteins in Protein Data Bank (PDB; pdb.org/pdb/home/home.do).Typically, four to five thousand variants per library were screened forkinetic and insensitivity parameters. Genes coding for shuffled variantsof HPPD were expressed in E. coli. The library was plated out on richagar medium, and individual colonies were picked and grown in richmedium. Colonies with active HPPD enzyme cause the medium to turn browndue to the conversion of homogentisate to a brown ochronotic pigment(Zannoni V G et al., 1969). Proteins with the ability to turn the mediumbrown in the presence of 100 μM mesotrione in rounds 1 to 6 ortembotrione in rounds 7 and 8 were subjected to detailed analysis.Kinetic characteristics of k_(ON), k_(OFF), k_(cat) and K_(m) weredetermined (Table 2).

The diversity of substitutions identified through phylogenetic sequencediversity, random mutagenesis, site-directed mutagenesis, and structuralfeatures based on crystal structures of proteins in Protein Data Bank(PDB; pdb.org/pdb/home/home.do in the improved HPPD enzymes of thisstudy is listed in Table 3 and 3b. Diversity not accessible throughthese methods but identified by saturation mutagenesis are shown inExample 7. Table 3 shows exemplary diversity contributing to improvementof insensitive maize HPPD. Indicated amino acids are neutral orbeneficial to HPPD fitness. Table 3b shows diversity identified bysaturation mutagenesis of Round 7, variant 9070 (SEQ ID NO:2) andfitness (ON rate ratio×OFF rate ratio×k_(cat)/K_(m)) relative to Round7, variant 9070 (SEQ ID NO:2) for the inhibitors indicated therein.Native maize wild-type sequence is shown for comparison. In many cases asingle substitution was identified, while at other positions, manyneutral or beneficial substitutions were identified. The additionalincrement of enzyme fitness seen in round 8 (Table 2; FIGS. 5 and 6) wasattained through mutations not present in the natural diversity, butaccessed only through saturation mutagenesis. The variant with thehighest fitness parameter, Round 8, variant 1973 (SEQ ID NO:8), had 26amino acid substitutions relative to native maize HPPD.

TABLE 3 Position 32 40 42 44 46 47 68 71 98 114 Maize WT N S R H L A G AF A Diversity R A H VG V S A V L S QSC LI Position 120 122 125 137 144146 150 161 167 175 Maize WT A A R V A D A G R E Diversity P T S I V V SS G G Position 184 187 193 202 207 209 211 219 221 225 Maize WT Y Y G GG A Y I G E Diversity F H D R D V C VLM VASC D Position 226 233 241 253260 261 262 268 278 282 Maize WT L F E A M V L N H R Diversity M VCL G TVLI A WI G R K MI Position 289 291 301 303 316 320 327 328 330 331Maize WT F D M L Q A M A P T Diversity Y E I V RK S L P R GQPLH Position341 347 352 360 377 382 383 387 395 405 Maize WT R T K L V T L I E KDiversity DEA S DEN M LI A F M G E CI Position 414 417 418 425 437 438440 442 443 444 Maize WT G S Q D A A A Q G S Diversity DTFV G E E P ETVK A Q G QASR MHYK

TABLE 3b ON × OFF × kcat/km fold vs Round 7, variant 9070 Mutation*tembo meso DKN Topra Sulco Q366E 1.8 1.8 1.7 1.9 1.4 G417S 1.6 1.3 0.91.2 1.1 A432R 1.6 1.5 2.1 1.4 1.3 G417Q 1.5 1.5 1.0 1.4 1.2 L385V 1.41.0 1.1 1.3 1.0 P206Q 1.4 1.1 1.2 1.1 1.0 A432K 1.4 1.6 1.6 1.5 1.5S214N 1.3 1.1 1.4 1.2 1.1 L385I 1.3 1.1 1.2 1.2 1.1 P158K 1.3 1.0 1.01.1 0.9 E356R 1.2 1.1 1.1 1.1 1.1 E356K 1.2 1.2 1.1 0.9 1.1 R340K 1.21.3 2.2 1.1 1.3 I387L 1.1 1.3 1.6 1.0 1.3 Y211L 1.1 0.9 1.1 1.1 0.9Q434R 1.1 1.1 1.1 1.1 1.1 P206S 1.1 0.9 1.1 1.0 0.8 Q434H 1.1 1.3 1.41.1 1.3 A191G 1.0 1.1 1.1 1.1 1.1 L182M 1.0 0.8 0.9 0.9 0.9 *Mutationshown relative to Round 7, variant 9070 (SEQ ID NO: 2)

FIG. 5 illustrates the progression of desensitization to mesotrione fromwild type to the best variant that emerged from the round 8 library.Improved (slower) rates of association of enzyme and mesotrione,manifested in the assay as a higher value for ON rate ratio, werereadily attained. Values ranged from that of the wild type, 0.2, to thetheoretical maximum value of 1.0, meaning that the reaction withinhibitor did not measurably slow compared to the reaction with noinhibitor during the first 90 seconds. Improved (faster) rates ofdissociation were less common, being attained in the early rounds eithernot at all or at the expense of reduced catalytic efficiency. In theexamples shown in FIG. 5, catalytic efficiency was retained, but in thefirst 4 rounds of shuffling, OFF rate ratio actually decreased. However,variants with OFF rate ratios up to 0.7 were observed in rounds 5 to 8.Variants sufficiently improved in ON rate, OFF rate or both so as toresult in improved insensitivity parameter (ON rate ratio×OFF rateratio) included many with values in the range of 0.27 to 0.7,representing more than a 14-fold improved insensitivity compared tomaize wild-type HPPD (FIG. 5 and Table 2). No attempt was made toimprove k_(cat), but rather to find a sequence context in which improvedinsensitivity could be attained with little or no loss of enzymeturnover rate (k_(cat)) or catalytic efficiency (k_(cat)/K_(M)). Thenumber of mutations required was such that enzyme fitness(ON×OFF×k_(cat)/K_(M)) improved only 2-fold until round 5, but improvedanother 7- to 15-fold, depending on the inhibitor, in rounds 6 through8, for overall improvements of 20- and 35-fold for mesotrione andtembotrione, respectively (Table 2, FIG. 6).

Because there are diverse chemotypes among the registered herbicidalinhibitors of HPPD, a commercially valuable trait should confertolerance to most or all of these registered chemistries. To ensure thatdirected evolution met that criterion, parents for each successivelibrary were tested for insensitivity to the other inhibitors shown inFIG. 1, using the same procedures as for mesotrione. The result was thatimproved insensitivity, and hence enzyme fitness, obtained by selectionwith mesotrione or tembotrione was accompanied by improved insensitivityto all other inhibitors (FIG. 6).

Example 5. HPPD Expression Analysis in Soybean Plants

To mimic the pattern of expression with regard to growth stage, tissueand subcellular location, and uncharacterized signaling cues, thetransgene promoters were based on the native soybean HPPD promoter.Attempts to directly isolate or measure native HPPD protein accumulationindicated low abundance in leaves. This was confirmed by EST analysis.Profiles of transcript abundance in multiple tissues from soybean(SoyBase.org) were compared to other well-known herbicide target genes,EPSPS (glyphosate target) and ALS (ALS-inhibitor target) (FIG. 7). HPPDand EPSPS appear to be expressed at a low level in all tissues otherthan flowers compared to the well-characterized ACT2/7 gene (Hu et al.,2009). Preserving the native expression pattern for HPPD whilesubstituting the improved insensitive maize HPPD variant genes canconfer robust herbicide tolerance with only moderate overexpression ofthe transgene.

Example 6. Isolation and Characterization of the Soybean HPPD Promoter

A 1225 bp genomic sequence at the 5′ end of the G. max HPPD gene wasisolated, sequenced and subjected to promoter analysis using PromoterREAPer and Promoter Delineator (Simmons and Navarro Acevaedo, 2010).Five putative TATA boxes, GTATAAATAA (SEQ ID NO:95; TATA1), CCAATATATG(SEQ ID NO:96; TATA2), CCTTATATATC (SEQ ID NO:97; TATA3), TATATAATAA(SEQ ID NO:98; TATA4), and GAATATAAG (SEQ ID NO:99; TATA5) wereidentified as shown in FIG. 8A. The open reading frame starting from thefirst ATG after TATA3 encodes the 449 amino acid short protein. TATA2 iswithin the long protein transcript and TATA3 is embedded in the codingregion for the long protein. Based on the known transcripts, TATA5 andTATA3 appear to be best situated for the long and short transcripts,respectively. Each is situated approximately 35 nucleotides from thetranscription initiation as expected for eukaryotic promoters (Smale andKadonaga, 2003). Open reading frame (ORF) analysis of the longtranscript indicates a short ORF encoding 7 AAs starting at position−195. Downstream of this, the long ORF begins at position −99 andcontinues in frame comprising the short protein, which starts at +25. Aschematic of the G. max HPPD promoter, transcripts, and translationproducts is shown in FIG. 8B.

To evaluate the predicted TATA boxes for activity, 3′ deletions andvarious mutations of the promoter region were constructed and thefragments fused with DsRed2 for expression analysis using transientexpression in bushbean leaf tissue (Table 4). Table 4 showsrepresentative HPPD promoter activity data. DsRed2 measurements arerelative to full G. max HPPD promoter in extracts of bush bean leaves 3days after agro-infiltration with described promoter:DsRed2 fusionconstructs. The full promoter:DsRed2 construct with both transcriptsintact should produce both a 41 residue N-terminal HPPD:DsRed2 fusionprotein and the DsRed2 protein alone. The fluorescence value of thefusion protein was not measured in comparison to the DsRed2 protein. Itwas previously shown that the 41 amino acids fused to DsRed2 did producered fluorescence without conferring chloroplast localization (FIG. 4C).Deletion of a 613 bp DNA fragment upstream of the short proteintranscription start site, including all 5 putative TATA boxes, resultedin a DNA fragment that was not able to drive DsRed2 expression to alevel above the background. When TATA3 and the short transcript regionwere deleted with the DsRed2 initiating at the same position as the longprotein, 90% of the full promoter region accumulation of DsRed2 wasmeasured, showing the contribution of the upstream transcript. Toeliminate translation of the fusion protein and leave only thecontribution of the short protein, a stop codon was introduced upstreamof the DsRed2 start Only the short transcript DsRed2 would be translatedin this construct. The same amount of DsRed2 accumulated as when boththe fusion and the downstream DsRed2 could be translated. Thus, itappears that both transcripts are capable of supporting translationactivity but this activity is not additive. Total HPPD product from thenative promoter could be regulated via competition for transcriptionand/or translation. Deletions of TATA2 and 3, TATA2, 3, and 5, or TATA2,3, 4, and 5 abolished promoter activity. It was unexpected that deletionof TATA2 and 3 did not default to TATA5 and the upstream (−237)transcription initiation for DsRed2 expression (see FIG. 8 and Table 4).

TABLE 4 Average Relative Promoter Promoter Strength Promoter DescriptionVariant (%) Native G. max HPPD promoter region Gm HPPD 100 Deletionsseries Deletion of TATA2, TATA3, and TATA5 SHP000C 2 Deletion of all 5TATA SHP101C 0 Deletion of TATA 2, 3, 4, and 5 SHP102C 0 Deletion ofTATA3 SHP103C 90 Deletion of TATA2 and TATA3 SHP110C 3 Mutations inTATA3 A to C mutation in TATA3 SHP104C 23 T to C in TATA1 and A to C inTATA3 SHP105C 30 T to C in TATA1, T to G in TATA2, and A to C SHP106C 21in TATA3 TAT to GCA mutation in TATA3 SHP107C 15 ATA to CCG in TATA1 andTAT to GCA in SHP108C 19 TATA3 TAT to CAG in TATA5, TAT to GCA in TATA3SHP114C 11 Mutations in other TATA boxes TAT to CAG mutation in TATA2SHP111C 93 TAT to CAG mutation in TATA4 SHP112C 97 TAT to CAG mutationin TATA5 SHP113C 89 Point mutation to eliminate upORF start codonSHP120C 105 Point mutation to insert stop codon just SHP121C 92 upstreamof + 1 transcription start site Synthetic promoters Deletion of all 5TATA + element I^(a) SHP101 3 Deletion of TATA 2, 3, 4, and 5 + elementI SHP102 4 Deletion of TATA3 + element I SHP103 310 T to C in TATA1, Tto G in TATA2, and A to C SHP106 377 in TATA3 + element I TAT to GCAmutation in TATA3 + element I SHP107 129 Deletion of all 5 TATA +element II^(b) SHP201 23 Deletion of TATA3 + element II SHP203 272 T toC in TATA1, T to G in TATA2, and A to C SHP206 195 in TATA3 + element II^(a)Element I is a synthetic core promoter sequence derived fromSequence 1 in Bowen et al., 2000 ^(b)Element II consists of Element 1plus a transcription enhancer region called Rsyn7 derived from Sequence2 in Bowen et al., 2000.

A second method to characterize the role of the predicted TATA sequenceswas mutagenesis of the specific sequences, changing either 1 or 3nucleotides. In all cases, if TATA3 was mutated, no matter what othermutations were present, promoter activity was reduced by 70-90%. Atriplet nucleotide change reduced the activity more than a singlenucleotide change. Triplet nucleotide mutations in either TATA2, TATA4,or TATA5 showed little or no effect on accumulation when DsRed2 replacedthe short protein open reading frame. Upstream ORFs have been shown toreduce both transcription and translation in plant genes (Saul et al.,2009). A mutation to eliminate the ATG start codon of the HPPD upORF didnot have any affect as DsRed2 was within 5% of that measured with theunaltered promoter construct. Both deletion and mutation analysisprovide evidence that TATA3 is important in maintaining full activity ofthe soy HPPD promoter but, because deletion of the TATA3 sequencealtogether still leaves 90% promoter activity, other elements are alsofunctional.

Example 7. Derivations of Soybean HPPD Promoter for Transgene Expression

To create transgene expression cassettes for HPPD inhibitor herbicidetolerance in soybean, cassettes were constructed with the intention ofmaintaining the HPPD regulatory information while modestly increasingthe expression level. In one case, the inactive fragment with deletionof TATA3, 2 and 5 was fused with a synthetic core promoter sequence(Element I in Table 4, Bowen et al., 2000; sequence 1) followed by the45 bp 5′UTR sequence including the predicted transcription start sitefrom the soybean native HPPD gene comprising the nucleotides betweenTATA3 and ATG. In other cases either TATA3 or TATA5 were replaced withthe synthetic core promoter to drive the short or long transcripts at anincreased level. DsRed2 fusion constructs with these promoters showedthat inclusion of the synthetic TATA region resulted in two- tothree-fold increased DsRed2 accumulation (Table 4). The 35S enhancerregion (Ow et al., 1987) at the 5′ end of the altered promoter fragmentsor an enhancing region called Rsyn7 containing OCS transcription factormotif sequences (Element II in Table 4, Bowen et al., 2000; sequence 2)near the core TATA box were added to increase expression. Planttransformation constructs were designed either with full-lengthinsensitive maize HPPD in combination with promoters giving rise to onlyone transcript or with the N-terminal 86 amino acids of the longchloroplast targeting sequence of G. max followed by the conservedmature maize HPPD protein starting at amino acid 50 (FIG. 4F). Thelatter was designed to provide dual targeting of a highly insensitiveHPPD enzyme. Final functional validation of the promoter/CTP/variantHPPD cassettes was by herbicide tolerance efficacy testing of transgenicsoybean plants.

Example 8. Generating and Identifying Beneficial Novel Amino AcidDiversity

Saturation Mutagenesis of Maize HPPD

The backbone gene for saturation mutagenesis was Round 7, variant 9070(SEQ ID NO:2), which had the highest fitness parameter with inhibitorssuch as mesotrione and tembotrione among the variants generatedpreviously (US20120042413(A1). Libraries were created for each positionin the Round 7, variant 9070 (SEQ ID NO:2) using NNK (where N representsa 25% mix each of adenine, thymine, guanine, and cytosine nucleotides;and K represents a 50% mix each of thymine and guanine nucleotides) asthe degenerate codon for the position to be mutagenized. PCR reactionmixtures contained a mutagenic forward primer (NNK codon flanked by 28nucleotides matching with template at each side of the NNK) and areverse primer that was the complement of the sequence preceding theforward primer, 28 nucleotides in length. To eliminate the mis-matchedbubble, a second PCR reaction was performed with a forward, resolutionprimer that matched the 28 nucleotides of the template upstream of theNNK site, and the same reverse primer as in the first reaction. Thetemplate for the second PCR reaction was the product of the first,diluted 10-fold. To make circular double stranded DNA plasmids from theblunt ended PCR products, the products were digested with T4polynucleotide kinase, T4 DNA ligase, and DpnI (to disrupt the parentalDNA template). After desalting by μtltrafiltration, the ligationproducts were ready for transformation and downstream applications.

The transformation mixture for each position mutagenized was plated onLB agar containing kanamycin. 47-94 colonies from each plate were pickedinto LB liquid, in 96-well format. The cells were sub-cultured into 2×YTmedium unmodified, or containing 50 μM tembotrione or 100 μM mesotrioneand evaluated by their ability to turn the medium brown, as described inExample 1. Wells in which the medium turned as brown as or browner thanthe Round 7, variant 9070 (SEQ ID NO:2) controls were selected as hits.The amino acid substitutions in Round 7, variant 9070 (SEQ ID NO:2) ofthe 554 variants selected as hits are listed in Megatable 1. Sequencingof entire plates selected at random indicated that on average, 17 aminoacid substitutions were accessed per position.

The variants selected in the medium browning screen were expressed in E.coli and purified as described in Example 1, then evaluated for affinityfor tembotrione by obtaining the ON and OFF rate ratios described inExample 1. The results for insensitivity evaluation (ON and OFF rateratio) of 119 single substitutions (relative to Round 7, variant 9070(SEQ ID NO:2)) selected from medium browning in the presence of 100 μMtembotrione are shown in Table 5.

TABLE 5 Parameters with ON x ON x OFF x tembotrione OFF, kcat Substi-k_(cat) ON OFF ON x fold vs Fold tution min⁻¹ ratio ratio OFF wt Valuevs wt 331N 40.4 0.75 0.43 0.32 63.0 12.99 12.14 438G 33.8 0.74 0.42 0.3160.3 10.41 9.73 331R 30.3 0.73 0.38 0.28 54.6 8.44 7.89 437K 35.7 0.760.36 0.27 52.9 9.63 9.00 438R 29.2 0.75 0.33 0.25 48.5 7.23 6.76 385V21.4 0.75 0.33 0.25 48.2 5.26 4.92 376W 23.1 0.68 0.34 0.23 46.0 5.425.07 417S 18.5 0.82 0.28 0.23 45.2 4.26 3.98 161E 17.2 0.78 0.29 0.2344.8 3.92 3.67 161Q 27.7 0.77 0.30 0.23 44.8 6.33 5.91 439R 24.7 0.730.30 0.22 43.3 5.45 5.09 161S 24.5 0.76 0.29 0.22 43.2 5.41 5.06 182M26.0 0.79 0.28 0.22 42.5 5.63 5.26 171F 16.6 0.75 0.28 0.21 41.8 3.543.31 215G 24.4 0.79 0.27 0.21 41.8 5.19 4.85 191S 12.4 0.75 0.28 0.2140.8 2.59 2.42 158K 50.4 0.77 0.27 0.21 40.6 10.44 9.76 332A 41.5 0.750.28 0.21 40.5 8.58 8.02 161Y 21.6 0.78 0.26 0.20 40.0 4.40 4.11 385I27.5 0.75 0.27 0.20 39.5 5.55 5.18 331G 29.0 0.73 0.27 0.20 39.1 5.785.40 161N 23.5 0.78 0.25 0.20 38.6 4.63 4.33 417Q 20.6 0.74 0.27 0.2038.4 4.04 3.77 161L 14.0 0.77 0.25 0.19 37.8 2.71 2.53 159C 21.0 0.790.24 0.19 37.6 4.03 3.77 166P 11.4 0.77 0.25 0.19 37.2 2.17 2.03 166A23.1 0.77 0.24 0.19 36.4 4.29 4.01 331D 32.4 0.75 0.25 0.18 36.2 5.985.59 169H 13.8 0.75 0.25 0.18 36.0 2.54 2.38 366E 20.1 0.75 0.24 0.1834.9 3.58 3.35 382S 29.6 0.71 0.24 0.17 33.0 4.97 4.65 360L 26.5 0.770.22 0.17 32.6 4.41 4.12 390N 30.3 0.75 0.22 0.17 32.4 5.00 4.67 189P26.2 0.76 0.22 0.16 32.3 4.31 4.02 358E 15.5 0.69 0.23 0.16 31.5 2.492.33 356K 38.8 0.75 0.21 0.16 31.2 6.18 5.78 206Q 35.4 0.74 0.21 0.1630.8 5.57 5.20 191L 21.5 0.77 0.20 0.16 30.5 3.35 3.13 432R 30.6 0.780.20 0.16 30.4 4.75 4.44 356R 39.1 0.75 0.21 0.15 30.0 5.97 5.58 205T25.1 0.74 0.20 0.15 29.0 3.72 3.48 340K 44.7 0.75 0.20 0.15 28.7 6.566.13 376V 31.0 0.71 0.21 0.15 28.7 4.53 4.23 206S 35.5 0.75 0.20 0.1528.5 5.15 4.82 437F 12.7 0.76 0.19 0.14 28.1 1.82 1.70 214N 35.4 0.760.19 0.14 27.9 5.04 4.71 399Y 27.8 0.71 0.20 0.14 27.9 3.95 3.70 357Y28.7 0.72 0.20 0.14 27.5 4.03 3.76 399H 28.8 0.72 0.19 0.14 27.4 4.023.75 387L 33.3 0.75 0.19 0.14 27.0 4.58 4.28 352K 32.2 0.70 0.19 0.1326.2 4.30 4.02 221V 9.8 0.75 0.18 0.13 26.1 1.30 1.21 437V 19.9 0.670.20 0.13 26.0 2.63 2.46 432K 31.5 0.76 0.17 0.13 25.7 4.13 3.86 399N37.4 0.75 0.17 0.13 25.2 4.81 4.50 396V 29.0 0.72 0.18 0.13 25.2 3.733.49 211L 36.9 0.77 0.17 0.13 25.0 4.72 4.41 217Y 20.7 0.76 0.17 0.1324.9 2.63 2.45 431F 28.9 0.80 0.16 0.13 24.5 3.61 3.37 195E 16.6 0.690.18 0.12 24.4 2.07 1.93 231S 20.9 0.68 0.18 0.12 23.8 2.54 2.37 399R34.8 0.74 0.17 0.12 23.6 4.18 3.91 200C 21.4 0.73 0.16 0.12 23.6 2.572.40 396T 37.7 0.71 0.17 0.12 23.5 4.51 4.22 187M 23.5 0.70 0.17 0.1223.2 2.78 2.60 227G 34.6 0.79 0.15 0.12 23.2 4.09 3.83 432V N.A. 0.670.17 0.12 23.1 0.00 0.00 190M 17.7 0.71 0.16 0.12 22.9 2.07 1.93 375L36.1 0.71 0.16 0.12 22.8 4.20 3.92 352R 39.4 0.75 0.15 0.11 21.9 4.404.11 202T 13.1 0.70 0.16 0.11 21.9 1.46 1.36 399Q 36.1 0.72 0.15 0.1121.5 3.96 3.70 202A 12.0 0.69 0.16 0.11 21.5 1.32 1.23 396M 35.4 0.730.15 0.11 21.4 3.86 3.61 399S 35.8 0.70 0.15 0.11 21.3 3.90 3.64 434R52.1 0.73 0.15 0.11 21.2 5.63 5.26 221A 42.2 0.62 0.17 0.10 20.3 4.374.09 195V 20.1 0.73 0.14 0.10 20.2 2.07 1.93 214T 39.2 0.74 0.14 0.1020.2 4.03 3.76 191G 42.6 0.77 0.13 0.10 20.1 4.36 4.08 206K 21.9 0.740.14 0.10 19.9 2.23 2.08 342V 40.6 0.78 0.13 0.10 19.7 4.08 3.82 398D38.7 0.72 0.14 0.10 19.6 3.87 3.62 434H 51.9 0.78 0.13 0.10 19.5 5.164.82 193Q 23.9 0.77 0.13 0.10 19.3 2.35 2.20 189E 21.6 0.72 0.14 0.1019.2 2.11 1.98 211S 18.9 0.79 0.12 0.10 19.1 1.83 1.71 190E 27.2 0.720.13 0.10 18.7 2.59 2.42 190T 28.0 0.75 0.13 0.10 18.6 2.66 2.48 396L40.5 0.57 0.17 0.09 18.6 3.85 3.60 432S 34.6 0.72 0.13 0.09 18.6 3.283.06 056S 41.9 0.78 0.12 0.09 18.5 3.97 3.71 423W 36.7 0.48 0.19 0.0918.0 3.37 3.15 383M 45.9 0.70 0.13 0.09 17.5 4.11 3.84 206L 18.3 0.760.12 0.09 17.3 1.62 1.51 383L 47.2 0.66 0.13 0.08 16.3 3.92 3.67 192V17.6 0.73 0.11 0.08 16.2 1.45 1.36 342M 52.3 0.73 0.11 0.08 16.0 4.284.00 125L 37.3 0.76 0.11 0.08 16.0 3.04 2.84 432L 30.7 0.67 0.12 0.0815.7 2.47 2.30 413A 39.0 0.59 0.13 0.08 15.5 3.09 2.88 214R 25.4 0.750.10 0.08 14.9 1.94 1.81 434L 55.5 0.71 0.11 0.08 14.8 4.20 3.93 053F47.0 0.75 0.10 0.08 14.8 3.54 3.31 349Q 42.6 0.76 0.10 0.07 14.7 3.192.98 434K 58.5 0.70 0.11 0.07 14.5 4.33 4.05 398A 42.8 0.72 0.10 0.0714.4 3.14 2.93 342C 71.5 0.71 0.10 0.07 14.0 5.09 4.76 381N 55.8 0.740.10 0.07 13.7 3.91 3.66 227E 27.5 0.72 0.10 0.07 13.7 1.93 1.80 375R71.8 0.60 0.10 0.06 12.1 4.43 4.14 373V 49.2 0.76 0.08 0.06 12.0 3.012.81 349E 47.9 0.76 0.08 0.06 11.6 2.84 2.65 429G 50.2 0.74 0.08 0.0611.6 2.97 2.78 234K 33.8 0.65 0.09 0.06 11.6 2.00 1.87 429T 53.7 0.720.08 0.06 11.5 3.16 2.95 202K 9.2 0.61 0.09 0.06 11.3 0.53 0.50 214M22.6 0.74 0.07 0.06 10.9 1.25 1.17 418E 83.8 0.69 0.05 0.04 7.1 3.032.83 Zm wt 210 0.17 0.03 0.0051 1.00 1.07 1.00 9070 34.2 0.74 0.21 0.1530.0 5.25 4.90

Thirty nine variants were desensitized to tembotrione compared with thebackbone enzyme, Round 7, variant 9070 (SEQ ID NO:2) and all weredesensitized compared with maize wild type HPPD (SEQ ID NO: 1). Becausethe assay for ON rate ratio includes an initial rate measurement atsaturating hydroxyphenylpyruvate without inhibitor and with known enzymeconcentration, an estimate of k_(cat) was available. Taking into accountk_(cat) and insensitivity parameters, 30 variants were selected formeasurement of substrate saturation kinetic parameters and re-evaluationof insensitivity to tembotrione. The kinetic and insensitivityparameters were determined as described in Example 1, and weremultiplied to generate the “trait fitness” parameter. The complete listof variants, i.e., of selected single substitutions in SEQ ID NO:2,analyzed with multiple inhibitors and the results obtained are shown inTable 6. The same set of 30 variants were evaluated for insensitivity tomesotrione, sulcotrione, isoxaflutole (its active diketonitrile form,abbreviated DKN in Table 6) and topramezone.

All variants desensitized to tembotrione were desensitized to all otherinhibitors, but not to the same magnitude or proportion. Foldimprovement with tembotrione and diketonitrile (Trait fitness for themutant/Trait fitness for maize wild type) was generally greater thanwith mesotrione or sulcotrione because the native maize HPPD was alreadyless sensitive to inhibition by the latter two inhibitors. Further, eachvariant was not proportionately desensitized to all inhibitors. Whentrait fitness for tembotrione is plotted versus trait fitness for theother inhibitors, the correlation coefficients (R² value) obtained are0.74 with mesotrione, 0.64 with sulcotrione, 0.86 with diketonitrile and0.94 with topramezone (data not shown). These results show that althoughbeneficial substitutions identified by selection with one inhibitoraccrues benefits with other inhibitors, though selection with inhibitorsoutside of those used here may result in a different set of preferredsubstitutions.

TABLE 6 Kinetic parameters Insensitivity parameter, ON x OFF Traitfitness, ON x OFF x k_(cat)/K_(M) Substi- k_(cat), K_(M) Tembo- Meso-Sulco- Topra- Tembo- Meso- Sulco- Topra- tution min⁻¹ (uM) k_(cat)/K_(M)trione trione trione DKN mezon trione trione trione DKN mezon 366E 38.81.61 24.1 0.33 0.78 0.74 0.44 0.48 8.0 18.7 17.8 10.6 11.6 417Q 33.51.56 21.5 0.33 0.73 0.74 0.39 0.39 7.0 15.8 15.8 8.4 8.4 432R 56.7 1.9728.8 0.23 0.53 0.59 0.27 0.31 6.7 15.2 17.0 7.8 8.8 432K 67.5 2.08 32.40.21 0.52 0.59 0.26 0.29 6.7 17.0 19.2 8.5 9.4 417S 26.7 1.41 18.9 0.330.67 0.77 0.41 0.41 6.2 12.6 14.5 7.7 7.8 214N 84.6 3.62 23.4 0.25 0.480.59 0.33 0.32 5.8 11.2 13.8 7.6 7.5 385I 46.1 2.29 20.1 0.28 0.56 0.700.41 0.38 5.6 11.4 14.2 8.2 7.6 158K 47.1 2.49 18.9 0.29 0.54 0.63 0.380.37 5.5 10.3 12.0 7.1 7.1 385V 30.3 1.91 15.9 0.34 0.65 0.78 0.33 0.495.4 10.3 12.4 5.2 7.8 191G 71.7 2.46 29.1 0.19 0.40 0.51 0.25 0.24 5.411.7 14.9 7.2 6.9 211L 77.6 3.2 24.2 0.22 0.37 0.47 0.25 0.27 5.4 9.111.5 6.1 6.5 340K 73.5 2.41 30.5 0.16 0.44 0.54 0.23 0.22 5.0 13.3 16.47.0 6.7 206Q 66.6 2.63 25.3 0.19 0.46 0.53 0.26 0.27 4.9 11.6 13.4 6.76.7 214T 84.2 2.94 28.6 0.17 0.41 0.50 0.21 0.23 4.8 11.7 14.3 6.1 6.5360L 32.6 1.71 19.0 0.25 0.51 0.63 0.34 0.32 4.8 9.7 12.0 6.5 6.0 434H84.5 2.77 30.5 0.15 0.46 0.55 0.21 0.22 4.7 14.1 16.7 6.5 6.7 387L 74.32.46 30.2 0.15 0.46 0.56 0.26 0.21 4.7 14.0 17.0 7.8 6.5 356K 65.8 2.625.3 0.18 0.48 0.55 0.25 0.23 4.5 12.2 13.9 6.3 5.8 356R 79.0 2.89 27.30.16 0.44 0.53 0.21 0.24 4.5 11.9 14.4 5.7 6.5 182M 56.1 2.88 19.5 0.230.44 0.60 0.30 0.29 4.5 8.7 11.7 5.9 5.7 434R 80.9 2.74 29.5 0.15 0.390.47 0.18 0.22 4.3 11.4 13.9 5.4 6.5 206S 67.9 3.36 20.2 0.20 0.46 0.530.29 0.29 4.1 9.4 10.7 5.9 6.0 191L 32.9 2.74 12.0 0.33 0.45 0.56 0.380.37 3.9 5.4 6.7 4.5 4.4 227G 45.3 2.61 17.4 0.22 0.52 0.63 0.26 0.283.7 9.0 10.9 4.5 4.9 390N 50.2 2.86 17.5 0.20 0.45 0.58 0.29 0.27 3.57.9 10.1 5.2 4.7 342V 54.2 2.59 20.9 0.17 0.42 0.51 0.22 0.23 3.5 8.710.6 4.6 4.7 431F 30.8 1.77 17.4 0.19 0.53 0.59 0.26 0.27 3.4 9.2 10.34.6 4.7 189P 41.8 3.35 12.5 0.25 0.51 0.62 0.32 0.31 3.1 6.3 7.7 4.0 3.9205T 34.4 2.72 12.6 0.22 0.47 0.60 0.30 0.29 2.8 6.0 7.6 3.8 3.7 376W36.1 5.51 6.5 0.31 0.39 0.16 0.37 0.32 2.1 2.5 1.1 2.4 2.1 9070 55.12.35 23.4 0.19 0.45 0.56 0.24 0.26 4.4 10.5 13.0 5.6 6.2 Zm wt 219 6.434.2 0.0051 0.0437 0.0872 0.0096 0.0154 0.174 1.494 2.981 0.328 0.525

Example 9. Combining Beneficial Diversity to Optimize Fitness

To extend the benefits of the single substitutions identified in Example2, twenty of the most preferred substitutions distributed among 14positions in were selected for construction of a combinatorial library.The best of these, Q366E, was selected as the backbone for a library inwhich the remaining 19 substitutions were allowed to combine randomly.To construct the libraries, the technique of semi-synthetic shufflingwas used, as described earlier (Ness J E et al., Nature Biotech 20,1251-1255, 2002). Two libraries were made in which the frequency ofmutations averaged 2.7 or 4.1 per gene and screened for insensitivity totembotrione, as described in Example 2. Insensitivity parameters fortembotrione and k_(cat) of 77 variants obtained from saturationmutagenesis followed by combinatorial shuffling and selected from themedium browning screen are shown in Table 7.

TABLE 7 Seq ON x ID ON rate OFF rate ON x OFF x NO. Variant name ratioratio OFF kcat kcat 1 Mz wt 0.213 0.033 0.007 97.4 0.68 2 9070 0.7440.116 0.086 40.0 3.45 3 9070Q366E 0.760 0.273 0.208 20.1 4.18 4P056028-A-01 0.697 0.249 0.173 39.1 6.78 5 P056028-A-02 0.680 0.3870.263 38.6 10.15 6 P056028-F-05 0.700 0.395 0.276 27.4 7.57 7P056028-G-01 0.742 0.320 0.238 32.2 7.65 8 P056028-G-01R 0.719 0.2800.201 70.8 14.24 9 P056028-B-02 0.800 0.469 0.375 28.2 10.58 10P056028-F-01 0.718 0.304 0.218 31.3 6.82 11 P056028-D-08 0.681 0.3610.246 27.5 6.77 12 P056028-E-04 0.740 0.360 0.267 19.2 5.13 13P056028-A-06 0.760 0.281 0.214 27.0 5.77 14 P056028-F-02 0.730 0.4300.314 28.2 8.84 15 P056028-C-01 0.742 0.310 0.230 25.9 5.95 16P056028-E-02 0.761 0.326 0.248 23.6 5.86 17 P056028-C-07 0.714 0.3820.273 21.2 5.80 18 P056028-A-03 0.748 0.243 0.181 24.0 4.36 19P056028-C-05 0.715 0.375 0.268 21.7 5.80 20 P056028-A-08 0.669 0.3240.217 26.2 5.68 21 P056028-D-03 0.770 0.453 0.349 19.6 6.83 22P056028-B-09 0.648 0.187 0.121 34.5 4.19 23 P056028-A-10 0.707 0.3670.260 16.8 4.35 24 P056028-A-11 0.706 0.366 0.258 8.6 2.21 25P056028-A-04 0.724 0.133 0.096 11.1 1.06 26 P056028-A-05 0.707 0.2800.198 17.7 3.50 27 P056028-A-07 0.726 0.329 0.239 19.5 4.65 28P056028-A-09 0.692 0.339 0.235 13.9 3.26 29 P056028-B-01 0.745 0.3090.230 18.6 4.28 30 P056028-B-10 0.703 0.327 0.230 17.9 4.12 31P056028-B-03 0.732 0.353 0.259 17.9 4.63 32 P056028-B-04 0.718 0.2730.196 16.5 3.24 33 P056028-B-05 0.734 0.287 0.211 18.3 3.85 34P056028-B-06 0.713 0.353 0.252 20.0 5.03 35 P056028-B-07 0.788 0.3890.307 9.2 2.83 36 P056028-B-08 0.681 0.325 0.221 15.5 3.44 37P056028-C-10 0.699 0.356 0.249 14.6 3.63 38 P056028-C-11 0.731 0.2930.214 12.3 2.64 39 P056028-C-02 0.717 0.379 0.272 18.8 5.11 40P056028-C-03 0.739 0.356 0.263 13.7 3.62 41 P056028-C-04 0.727 0.3220.234 22.7 5.32 42 P056028-C-06 0.742 0.351 0.261 10.6 2.77 43P056028-C-08 0.712 0.381 0.271 13.5 3.65 44 P056028-C-09 0.706 0.3140.222 17.0 3.76 45 P056028-D-01 0.728 0.348 0.254 21.3 5.39 46P056028-D-10 0.670 0.253 0.170 18.1 3.07 47 P056028-D-11 0.719 0.2610.188 17.1 3.21 48 P056028-D-02 0.730 0.299 0.218 24.3 5.31 49P056028-D-04 0.696 0.197 0.137 12.4 1.71 50 P056028-D-05 0.730 0.5080.371 12.6 4.66 51 P056028-D-06 0.731 0.424 0.310 9.9 3.07 52P056028-D-07 0.775 0.370 0.286 9.1 2.60 53 P056028-D-09 0.652 0.3710.242 13.0 3.16 54 P056028-E-10 0.702 0.339 0.238 11.5 2.73 55P056028-E-11 0.721 0.304 0.219 16.9 3.70 56 P056028-E-03 0.735 0.4120.303 16.9 5.10 57 P056028-E-05 0.704 0.325 0.229 15.2 3.48 58P056028-E-06 0.346 0.186 0.064 28.2 1.76 59 P056028-E-07 0.585 0.2620.153 20.6 3.08 60 P056028-E-08 0.685 0.410 0.281 12.6 3.55 61P056028-E-09 0.676 0.308 0.208 14.9 3.10 62 P056028-F-10 0.726 0.2910.211 13.7 2.89 63 P056028-F-11 0.706 0.322 0.228 22.1 5.04 64P056028-F-03 0.738 0.491 0.363 13.0 4.73 65 P056028-F-04 0.660 0.2450.161 16.7 2.70 66 P056028-F-06 0.739 0.305 0.225 14.5 3.25 67P056028-F-07 0.735 0.322 0.236 21.4 5.04 68 P056028-F-08 0.705 0.3770.266 12.1 3.23 69 P056028-F-09 0.700 0.360 0.252 17.1 4.30 70P056028-G-10 0.607 0.259 0.157 29.3 4.61 71 P056028-G-02 0.761 0.3040.231 23.0 5.30 72 P056028-G-04 0.752 0.248 0.186 13.6 2.54 73P056028-G-05 0.739 0.361 0.267 16.7 4.47 74 P056028-G-06 0.725 0.3820.277 12.0 3.30 75 P056028-G-07 0.702 0.304 0.213 15.3 3.23 76P056028-G-08 0.737 0.379 0.279 11.8 3.29 77 P056028-G-09 0.716 0.3850.275 15.8 4.37Combinatorial variants exhibiting insensitivity and k_(cat) near thoseof the backbone sequence were further analyzed for kinetic parameters(k_(cat) and K_(M) obtained by substrate saturation kinetic analysis)and insensitivity parameters for mesotrione, sulcotrione, topramezoneand the diketonitrile form of isoxaflutole. Trait fitness ofcombinatorial variants of HPPD were compared with wild type and Round 7,variant 9070 (SEQ ID NO:2; see Table 8). The data show that whenvariants composed of random combinations of single substitutions wereselected based on fitness with tembotrione, fitness for the otherinhibitors was also improved.

TABLE 8 SEQ Insensitivity, tembotrione Insensitivity, mesotrione IDKinetic parameters Rate ratio Trait Rate ratio Trait NO Variant Namek_(cat) K_(M) k_(cat)/K_(M) ON OFF ONxOFF fitness ON OFF ONxOFF Fitness22 P056028-B-09 93.2 3.00 31.6 0.75 0.35 0.26 8.28 0.67 1.00 0.67 21.2 4P056028-A-01 72.4 2.49 29.1 0.84 0.43 0.36 10.43 0.67 1.00 0.67 19.6 18P056028-A-03 62.8 2.98 21.0 0.80 0.40 0.32 6.81 0.70 1.00 0.70 14.8 21P056028-D-03 44.2 2.08 21.3 0.77 0.45 0.35 7.44 0.68 1.00 0.68 14.5 9P056028-B-02 58.7 3.00 19.6 0.80 0.47 0.37 7.35 0.63 1.00 0.63 12.3 7P056028-G-01 41.4 2.06 20.4 0.77 0.47 0.36 7.32 0.71 1.00 0.71 14.6 8P056028-G-01R 70.8 2.02 35.3 0.72 0.28 0.20 7.09 0.73 1.00 0.73 25.6 12P056028-E-04 29.0 2.11 13.8 0.74 0.36 0.27 3.68 0.67 1.00 0.67 9.2 14P056028-F-02 45.5 2.22 20.5 0.73 0.43 0.31 6.43 0.67 1.00 0.67 13.7 5P056028-A-02 31.4 1.76 17.8 0.68 0.39 0.26 4.69 0.59 1.00 0.59 10.5 13P056028-A-06 74.6 4.05 18.4 0.76 0.28 0.21 3.94 0.63 0.74 0.47 8.6 6P056028-F-05 32.3 2.39 13.5 0.70 0.39 0.28 3.74 0.64 1.00 0.64 8.7 29070 88.9 2.91 30.7 0.80 0.22 0.17 5.36 0.66 0.89 0.59 18.1 3 9070Q366E30.8 1.57 19.5 0.82 0.33 0.27 5.25 0.72 1.00 0.72 14.0 1 Zm wt 219 6.4134.2 0.20 0.04 0.007 0.26 0.20 0.31 0.062 2.1 SEQ Insensitivity,sulcotrione Insensitivity, isoxaflutole (DKN) Insensitivity, topramezoneID Rate ratio Trait Rate ratio Trait Rate ratio Trait NO Variant Name ONOFF ONxOFF fitness ON OFF ONxOFF fitness ON OFF ONxOFF fitness 22P056028-B-09 0.78 0.88 0.68 21.6 0.77 0.33 0.25 7.93 0.80 0.48 0.3812.12 4 P056028-A-01 0.80 1.22 0.97 28.4 0.82 0.44 0.36 10.45 0.85 0.600.51 14.86 18 P056028-A-03 0.80 0.93 0.75 15.7 0.81 0.43 0.34 7.25 0.810.47 0.38 7.97 21 P056028-D-03 0.76 1.11 0.84 17.9 0.76 0.40 0.31 6.510.80 0.58 0.46 9.88 9 P056028-B-02 0.81 1.00 0.81 15.8 0.80 0.43 0.356.78 0.79 0.53 0.42 8.17 7 P056028-G-01 0.78 1.14 0.89 18.2 0.77 0.420.32 6.55 0.80 0.57 0.46 9.31 12 P056028-G-01R 0.75 1.11 0.83 11.5 0.770.38 0.29 3.98 0.81 0.53 0.43 5.91 14 P056028-E-04 0.72 1.09 0.79 16.10.75 0.42 0.31 6.44 0.80 0.60 0.48 9.85 5 P056028-F-02 0.69 1.28 0.8815.8 0.70 0.43 0.30 5.35 0.69 0.64 0.44 7.87 13 P056028-A-02 0.77 0.760.58 10.8 0.77 0.28 0.22 3.97 0.76 0.32 0.24 4.52 6 P056028-A-06 0.731.13 0.82 11.1 0.73 0.42 0.31 4.16 0.76 0.57 0.44 5.91 2 9070 0.81 0.710.38 11.8 0.82 0.20 0.11 3.30 0.79 0.25 0.13 3.99 3 9070Q366E 0.80 1.130.50 9.69 0.83 0.39 0.17 3.40 0.81 0.57 0.26 5.04 1 Zm wt 0.30 0.280.042 1.45 0.08 0.01 0.0005 0.015 0.100 0.045 0.002 0.077

Example 10. Tolerance to Multiple HPPD-Inhibiting Herbicides inTransformed Soybean

A 1228 bp genomic sequence at the 3′ end of the G. max HPPD gene wasisolated, sequenced and analyzed for promoter elements as describedearlier (US20120042414(A1). Elements were modified so as to decrease orincrease expression and various transformation cassettes, designed todirect a range of expression of shuffled maize HPPD, were constructed(see US Patent Publication US2012/0042414(A1). Transgenic soybean eventswere created using particle bombardment of embryogenic callus culturesand selection with either hygromycin or chlorsulfuron. T0 regeneratedplants were acclimated to greenhouse conditions in soil for two weeksand sprayed with two times labeled use rate of mesotrione. When siblingregenerants from the same event were available, the second plant wassprayed with 2× tembotrione. For each construct approximately 30 eventswere created with one or two copies of the HPPD insert at a singlelocus. To assess the expression cassettes, the number of events fromeach construct that showed 30% or less injury to 2× mesotrione and 2×tembotrione (on sibling plants) were counted. T0 plants were sampled forDNA analysis to verify single copy inserts and for protein analysis tomeasure HPPD accumulation in young leaves. Events with high injuryroutinely occurred due to the variability inherent in random genomicinsertion methods. Plants with less than 30% visible injury were grownto maturity and the T1 seeds that were harvested were sown in thegreenhouse or the field. The T1 plants were treated with 472 g/ha (4×field rate) mesotrione and screened by PCR to identify homozygotes.Tolerant, homozygous lines were grown and harvested for field trials.

A field trial performed in 2013 was designed to test: 1) variouspromoters known to drive a range of expression levels, described inUS20120042414(A1), and 2) two N-terminal variations of the HPPD protein9075 (SEQ ID NO:79), which is polypeptide sequence corresponding toRound 7, variant 9070 (SEQ ID NO:2) with R316 changed to Q. In one case,the N-terminus is that of the full-length enzyme. In the other case, thefirst 44 amino acids of SEQ ID NO:79 were replaced with the first 86amino acids of the long form of soy HPPD (see US Patent PublicationUS2012/0042412(A1)). Both N-termini were previously shown to directtransgenically expressed HPPD to both chloroplasts and cytosol (see USPatent Publication US2012/0042412(A1)). Transformation events fromseveral of the constructs were highly tolerant to mesotrione,tembotrione, and isoxaflutole at two to four times labeled fieldapplication rates.

For positive control comparisons, the strong synthetic viral-basedpromoters SUP and SCP1 (Bowen et al., 2000) were used to drive variousHPPD variants. Repeated occurrences of wrinkled leaf and chlorotic leafphenotypes along with occasional sterility in the SUP and SCP1 eventsindicated that these promoters were not suitable for commercial eventproduction. Measurements of HPPD protein accumulation in young leaves ofT0 plants as shown in Table 9 revealed that the strong syntheticpromoters accumulated HPPD protein near 1% of total soluble protein(10,000 ppm). The soybean derived HPPD promoters led to accumulation ofHPPD protein in tolerant events at levels in the range of 0.02-0.1%total soluble protein (200-1000 ppm). In general, promoters with addedsynthetic core elements and enhancers produced more tolerant events andmore protein than promoters with mutations and deletions. The lowerexpressing HPPD constructs provided higher recovery of phenotypicallynormal plants.

To look more closely at the role of the dual targeting of heterologousHPPD in soybean, constructs with N-terminal truncations (no targeting),truncated maize HPPD protein fused to known CTP elements (singletranscript), and soybean N-terminal 1-86 fused to truncated maize HPPDfor dual targeting were compared. All localization scenarios resulted inproduction of herbicide tolerant events, of varying efficacy (Table 9).Table 9 shows greenhouse characterization of T0 transgenic soybeanplants expressing HPPD cassettes with varied promoters and aninsensitive HPPD gene. Visual injury rating, 0 (no injury)-100 (dead)scale, average of 3 plots. DAT, days after treatment; All treatmentswere sprayed after two weeks acclimation from transformation (V2-V8) andincluded 0.25% v/v NIS and 8 lb/100 gal (NH₄)₂SO₄. Neither proteinaccumulation nor construct properties alone explain the spectrum ofvariability in green house T0 efficacy results. In all cases, however,tolerance to mesotrione at the maize field rate was more easily achievedthan tolerance to tembotrione.

TABLE 9 # % # % HPPD HPPD Events Events ≤30% Events Events ≤30% protein,ppm N-terminus 9075 meso injury tembo injury ave ≤30% Promoter fusionstart screen meso^(d) screen tembo^(e) injury⁶ SHP210^(a) GM-HPPD 50 15100 12 100 326 N1-86 SUP none 24 29 79 8 50 12779 SHP110^(b) GM-HPPD 5013 100 11 27 266 N1-86 SHP103C none 1 26 80 26 42 594 SHP106 6H1 CTP 246 100 5 0 69 SHP206^(c) none 1 22 86 na na 679 SHP110e^(c) GM-HPPD 50 4381 na na 876 N1-86 SHP111 GM-HPPD 50 37 70 13 7.7 318 N1-86 SHP120CGM-HPPD 50 57 61 31 3.2 165 N1-86 SHP110 GM-HPPD 50 13 38 1 0 382 N1-86SHP103C AT-RBCS 24 28 17 25 0 397 CTP ^(a)Promoter SHP210 has deletionof TATA5, 2 and 3 with insertion of Element II at the 3′ end of thepromoter. ^(b)Promoter SHP110 has deletion of TATA5, 2 and 3 withinsertion of Element I at the 3″ end of the promoter. ^(c)Constructevents tested in 2013 field tests. ^(d)210 g ai/ha mesotrione, evaluatedat 8 days after treatment ^(e)93 g ai/ha tembotrione, evaluated at 8days after treatment ^(f) Parts per million of total soluble protein.

Because T0 plants are heterozygous for the HPPD insert and because fieldconditions can be more stringent than greenhouse conditions, fieldtesting of homozygous lines is essential to fully evaluate the efficacyof the transgene traits. Field tests in 2013 with a round 6 desensitizedHPPD variant showed that several events created were highly tolerant tomesotrione, tembotrione, and isoxaflutole at 2× or 4× treatment levels.Some transient injury was apparent, but by 14 days after treatment, theplants were almost completely recovered as shown in FIG. 9. Tabulatedresults for 2 different events are shown in Table 10, which shows dataobtained from transgenic soybean plants expressing insensitive HPPDvariant constructs showing tolerance to three different HPPD-inhibitorherbicides in the field.

Seed were homozygous for single copy inserts in elite genetics. Visualinjury rating, 0 (no injury)-100 (dead) scale, average of 3 plots. Inthe table, the following abbreviations are used: DAT, days aftertreatment; 2× and 4×, treatment levels. All treatments were sprayed atthe V4 stage and included 0.25% v/v NIS and 8 lb/100 gal (NH₄)₂SO₄.

TABLE 10 Isoxaflutole Mesotrione Tembotrione Event Cassette DAT 2X 4X 2X4X 2X PRO206:FL9075 3 1 3 10 20 8 PRO206:FL9075 7 0.7 1.0 1.7 8.3 4.3PRO206:FL9075 14 0.0 0.0 0.0 3.3 1.0 PRO110e:Soy N-term 3 0 2 13 20 13PRO110e:Soy N-term 7 0.0 0.0 3.7 11.7 19.0 PRO110e:Soy N-term 14 0.0 0.00.0 0.7 4.0 PRO206: Promoter 206 described in US20120042414(A1) PRO110e:Promoter SHP110, described in US20120042414(A1) with the addition of aCaMV enhancer FL9075: Full-length shuffled maize variant 9075 (SEQ IDNO: 79) Soy N-term: 9075 (SEQ ID NO: 79) in which the first 44 aminoacids were replaced with the first 86 amino acids of the long form ofsoy HPPD (US20120042412(A1)) Mesotrione 1x = 0.105 lb ai/a = 118 g ai/haTembotrione 1x = 0.08 lb ai/a = 90 g ai/ha Isoxaflutole 1x = 0.06 lbai/a = 67 g ai/ha All treatments were at the V4 stage and included 0.25%v/v NIS and 8 lb/100 gal NH42SO4.

The data set from the field trial also illustrates the importance ofattaining an expression level that is neither too low nor too high. FIG.14 plots the efficacy of the transgenic trait, expressed as the visualrating of injury on a 100 scale as a function of the expression level,μg HPPD/g total protein. Excellent tolerance was obtained at a level of˜500-1000 μg/g, while lower expression results in more injury. However,perhaps because the HPPD reaction is practically irreversible and notinhibited by product, excessive catalytic capacity was associated withabnormal phenotypes such as chlorosis and leaf wrinkling (FIG. 14). Thedata show that symptoms are associated with high expression level.

The velocity of an enzyme catalyzed reaction is a function ofk_(cat)/K_(M), [E] and [S], where E is enzyme and S is substrate. Thesubstrate concentration in soybean tissues is unknown but presumed to beconstant, while enzyme concentration is determined by the expressionlevel. In the presence of inhibitor, the fraction of the enzyme that isfree to react with substrate is proportional to the K_(i) of theinhibitor. A common parameter used to quantify performance of an enzymein the presence of an inhibitor is k_(cat)/K_(M)×K_(i), which takes intoaccount catalytic efficiency and inhibitor affinity. An approximation ofthat expression is the “trait fitness” parameter,k_(cat)/K_(M)×(ON×OFF). Fitness times [E], or expression level,quantifies the expected performance in vivo, depending on substrate andinhibitor concentrations. Those are not known, but from the datapresented, an empirical estimate of the range of values for the quantity“fitness parameter”×“expression level” is the following:

-   -   Fitness range, 2 to 200 min⁻¹ uM⁻¹    -   Expression range, 200 to 2000 μg/g    -   Fitness×expression range, 400 to 400,000 min⁻¹ uM⁻¹

Example 11. Identification of Shuffled Variants of Maize HPPD forTolerance to as Vet Non-Commercialized Herbicidal Inhibitors

The value of the substitutions identified as beneficial fordesensitizing the enzyme to tembotrione is not limited to tembotrione,but extends to mesotrione, sulcotrione, topramezone and isoxaflutolediketonitrile. To discover a variant that confers tolerance to a newHPPD-inhibiting herbicide, the 554 single substitutions are screened bythe same tiered screen as in Examples 2 and 3. It is anticipated thatdifferent sets of preferred substitutions will emerge depending on thestructure of the inhibitor. The substitutions identified are thencombined randomly and the resulting library screened as described, andnovel recombinant variants selected for fitness to the novel compoundare identified. Thus, any of the 554 substitutions identified, eithersingly or in combination, can be useful in developing a tolerance traitfor future inhibitor classes.

For example, Round 6, variant 9070 (SEQ ID NO:2) and Round 8, variant1973 (SEQ ID NO:8) can be compared with maize wild type HPPD (SEQ IDNO:1) for their ability to catalyze the HPPD reaction in the presence ofadditional HPPD inhibiting compounds, e.g., compounds such as thosedepicted in FIGS. 1 and 16. Compounds such as those depicted in FIGS. 1and 16, can be purchased or synthesized following published synthesismethods. Enzymes are purified and kinetic and insensitivity parametersare determined as described in herein above. It is anticipated that thecatalytic efficiency as indicated by k_(cat)/K_(M) can be retainedthrough multiple rounds of shuffling, while insensitivity to additionalHPPD inhibitors can be increased, e.g., increased insensitivity to HPPDinhibitors depicted in FIGS. 1 and 16. Example 10 above describes afield trial in which a Round 6 HPPD variant expressed in soybean plantsprovided a high degree of tolerance to mesotrione, tembotrione andisoxaflutole. The most stringent condition for tolerance was a sprayrate of two times the labeled rate of tembotrione. Therefore, fitness ofthe Round 6 variant to tembotrione can be used as the minimal levelneeded for efficacy when expressed in a suitable expression construct,to which can be compared additional variants of HPPD obtained throughadditional rounds of shuffling. In addition, the insensitivity to thenovel HPPD inhibitors can be determined and shuffled variants selectedwherein the insensitivity to novel HPPD inhibitors is increased.

Megatable Legends

Megatable 1.

The definitions of the column headings are as follows: “MUT ID,” aunique identifier for each substitutions; “Position,” amino acidposition according to the numbering convention of SEQ ID NO:1, “RefA.A.,” the standard single letter code for the amino acid present in theSEQ ID NO:1 sequence at the indicated position; and “Substitution,” thestandard single letter code for the amino acid present in the mutantsequence at the indicated position.

Megatable 2.

The definitions of the column headings are as follows: “MUT ID,” aunique identifier for each substitutions; “Position,” amino acidposition according to the numbering convention of SEQ ID NO:1, “RefA.A.,” the standard single letter code for the amino acid present in theSEQ ID NO:1 sequence at the indicated position; and “Substitution,” thestandard single letter code for the amino acid present in the mutantsequence at the indicated position. The remaining column headings referto the kinetic parameters described herein above, i.e. “k_(cat)”indicates the parameter k_(cat); “ON rat.” Refers to the ON ratioparameter; “OFF rat.” refers to the OFF ratio parameter; “ON×OFF” refersto the calculated value that is the product of the ON ratio and OFFratio parameters; “Fold vs. wt” is the calculated increase in “ON×OFF”value versus the wild-type sequence, SEQ ID NO:1; “ON×OFF×k_(cat)”refers to the calculated value that is the product of the ON ratio, OFFratio, and k_(cat); and the last column with “Fold vs. wt” refers to thefold-increase in calculated value that is the product of the ON ratio,OFF ratio, and k_(cat) of the indicated mutant versus the wild-typesequence, SEQ ID NO:1.

Megatable 3.

The definitions of the column headings are as follows: “SEQ ID” is theSEQ ID NO for the sequences herein above; and “Variant name” is atrivial but unique name for the indicated sequence. The remaining columnheadings refer to the kinetic parameters described herein above, i.e.“ON ratio” Refers to the ON ratio parameter; “OFF ratio” refers to theOFF ratio parameter; “ON×OFF” refers to the calculated value that is theproduct of the ON ratio and OFF ratio parameters; “k_(cat)” indicatesthe parameter k_(cat); and “ON×OFF×k_(cat)” refers to the calculatedvalue that is the product of the ON ratio, OFF ratio, and k_(cat).

Megatable 1 Ref Activity MUT ID Position A.A. Substitution 1st tier 1 52E D + 2 52 E G + 3 52 E H + 4 52 E R + 5 52 E S + 6 52 E T + 7 53 L F +8 53 L I + 9 53 L M + 10 54 W C + 11 54 W L + 12 54 W Q + 13 55 C A + 1455 C G + 15 55 C T + 16 55 C V + 17 56 A H + 18 56 A L + 19 56 A N + 2056 A Q + 21 56 A S + 22 56 A T + 23 58 A G + 24 58 A T + 25 125 R L + 26147 A S + 27 148 F W + 28 148 F Y + 29 149 R A + 30 149 R I + 31 149 RK + 32 149 R M + 33 149 R P + 34 149 R S + 35 149 R T + 36 149 R V + 37149 R W + 38 152 V E + 39 153 A F + 40 153 A I + 41 153 A K + 42 153 AL + 43 153 A Q + 44 153 A R + 45 153 A T + 46 153 A V + 47 154 A C + 48154 A G + 49 154 A N + 50 154 A R + 51 154 A T + 52 157 R H + 53 157 RN + 54 157 R T + 55 157 R V + 56 158 P A + 57 158 P E + 58 158 P G + 59158 P K + 60 159 A C + 61 159 A M + 62 159 A S + 63 159 A T + 64 159 AV + 65 160 F L + 66 160 F M + 67 160 F Y + 68 161 G A + 69 161 G E + 70161 G L + 71 161 G M + 72 161 G N + 73 161 G P + 74 161 G Q + 75 161 GR + 76 161 G S + 77 161 G T + 78 161 G W + 79 161 G Y + 80 162 P T + 81163 V A + 82 163 V C + 83 163 V M + 84 163 V T + 85 164 D A + 86 164 DE + 87 164 D H + 88 164 D S + 89 164 D T + 90 165 L C + 91 165 L M + 92165 L V + 93 166 G A + 94 166 G P + 95 167 R + + 96 167 R V + 97 169 FA + 98 169 F H + 99 169 F W + 100 169 F Y + 101 170 R C + 102 170 R G +103 170 R I + 104 170 R K + 105 170 R L + 106 170 R M + 107 170 R P +108 170 R Q + 109 170 R S + 110 170 R T + 111 170 R V + 112 170 R W +113 171 L F + 114 171 L I + 115 171 L M + 116 171 L V + 117 172 A P +118 172 A R + 119 172 A S + 120 173 E P + 121 174 V C + 122 174 V I +123 175 E D + 124 175 E V + 125 175 E W + 126 175 E + + 127 176 L A +128 176 L M + 129 181 V F + 130 181 V I + 131 181 V M + 132 181 V N +133 182 L M + 134 187 Y C + 135 187 Y E + 136 187 Y G + 137 187 Y H +138 187 Y M + 139 187 Y V + 140 188 P D + 141 188 P G + 142 188 P Q +143 189 D E + 144 189 D P + 145 189 D S + 146 189 D T + 147 190 G A +148 190 G C + 149 190 G D + 150 190 G E + 151 190 G L + 152 190 G M +153 190 G N + 154 190 G P + 155 190 G Q + 156 190 G R + 157 190 G S +158 190 G T + 159 190 G V + 160 190 G W + 161 191 A E + 162 191 A F +163 191 A G + 164 191 A H + 165 191 A I + 166 191 A K + 167 191 A L +168 191 A M + 169 191 A N + 170 191 A R + 171 191 A S + 172 191 A T +173 191 A V + 174 192 A V + 175 193 G A + 176 193 G H + 177 193 G I +178 193 G L + 179 193 G P + 180 193 G Q + 181 193 G R + 182 193 G S +183 193 G T + 184 193 G V + 185 194 E D + 186 194 E L + 187 195 P A +188 195 P C + 189 195 P D + 190 195 P E + 191 195 P Q + 192 195 P S +193 195 P T + 194 195 P V + 195 196 F W + 196 200 F C + 197 202 G A +198 202 G E + 199 202 G K + 200 202 G L + 201 202 G T + 202 202 G V +203 202 G Y + 204 204 A C + 205 204 A D + 206 204 A E + 207 204 A G +208 204 A H + 209 204 A K + 210 204 A L + 211 204 A M + 212 204 A N +213 204 A Q + 214 204 A T + 215 204 A V + 216 205 S D + 217 205 S G +218 205 S L + 219 205 S Q + 220 205 S T + 221 205 S V + 222 206 P C +223 206 P D + 224 206 P K + 225 206 P L + 226 206 P Q + 227 206 P S +228 206 P T + 229 207 G Q + 230 207 G S + 231 207 G V + 232 208 A G +233 208 A H + 234 208 A Q + 235 208 A R + 236 208 A W + 237 209 A C +238 209 A D + 239 209 A E + 240 209 A G + 241 209 A I + 242 209 A K +243 209 A L + 244 209 A M + 245 209 A P + 246 209 A Q + 247 209 A S +248 209 A T + 249 209 A W + 250 210 D E + 251 210 D G + 252 210 D S +253 210 D T + 254 211 Y C + 255 211 Y F + 256 211 Y L + 257 211 Y S +258 211 Y W + 259 212 G K + 260 213 L W + 261 214 S K + 262 214 S M +263 214 S N + 264 214 S Q + 265 214 S R + 266 214 S T + 267 215 R A +268 215 R G + 269 217 D Q + 270 217 D Y + 271 220 V T + 272 221 G A +273 221 G F + 274 221 G H + 275 221 G I + 276 221 G L + 277 221 G M +278 221 G T + 279 221 G V + 280 222 N G + 281 222 N V + 282 227 A D +283 227 A E + 284 227 A G + 285 227 A I + 286 227 A K + 287 227 A L +288 227 A M + 289 227 A N + 290 227 A Q + 291 227 A R + 292 227 A S +293 227 A T + 294 227 A V + 295 229 A T + 296 230 A R + 297 230 A V +298 231 A C + 299 231 A H + 300 231 A L + 301 231 A S + 302 231 A T +303 233 M V + 304 234 A C + 305 234 A E + 306 234 A G + 307 234 A K +308 234 A L + 309 234 A M + 310 234 A Q + 311 234 A S + 312 234 A V +313 238 G S + 314 240 H R + 315 241 E A + 316 241 E D + 317 241 E G +318 241 E N + 319 241 E P + 320 241 E R + 321 241 E S + 322 241 E T +323 242 F A + 324 242 F D + 325 242 F S + 326 273 L V + 327 292 H N +328 331 L D + 329 331 L G + 330 331 L N + 331 331 L R + 332 332 S A +333 339 R K + 334 340 R E + 335 340 R K + 336 340 R N + 337 342 A C +338 342 A L + 339 342 A M + 340 342 A N + 341 342 A R + 342 342 A V +343 343 G R + 344 345 V I + 345 347 T S + 346 348 E Y + 347 349 A E +348 349 A Q + 349 349 A R + 350 349 A S + 351 351 I C + 352 351 I V +353 352 N E + 354 352 N K + 355 352 N L + 356 352 N Q + 357 352 N R +358 353 E L + 359 353 E M + 360 353 E S + 361 353 E T + 362 356 E K +363 356 E R + 364 357 L Y + 365 358 G E + 366 358 G R + 367 360 M L +368 360 M T + 369 364 D G + 370 364 D S + 371 364 D V + 372 365 D A +373 366 Q E + 374 368 V L + 375 369 L M + 376 369 L V + 377 372 I A +378 372 I K + 379 372 I Q + 380 372 I S + 381 372 I T + 382 373 F G +383 373 F L + 384 373 F R + 385 373 F V + 386 375 K L + 387 375 K R +388 376 P C + 389 376 P G + 390 376 P S + 391 376 P V + 392 376 P W +393 377 V E + 394 377 V G + 395 377 V L + 396 379 D K + 397 381 P N +398 382 T A + 399 382 T F + 400 382 T S + 401 383 F L + 402 383 F M +403 384 F W + 404 384 F Y + 405 385 L I + 406 385 L V + 407 386 E C +408 386 E I + 409 386 E V + 410 387 I G + 411 387 I L + 412 388 I L +413 388 I S + 414 388 I V + 415 389 Q G + 416 389 Q K + 417 389 Q T +418 390 R N + 419 391 I L + 420 391 I V + 421 392 G R + 422 392 G V +423 394 M I + 424 394 M K + 425 394 M L + 426 394 M Q + 427 394 M V +428 394 M Y + 429 395 E K + 430 395 E Q + 431 395 E S + 432 395 E V +433 396 K A + 434 396 K L + 435 396 K M + 436 396 K Q + 437 396 K R +438 396 K T + 439 396 K V + 440 397 D G + 441 397 D S + 442 398 E A +443 398 E D + 444 398 E G + 445 398 E P + 446 398 E S + 447 399 K A +448 399 K D + 449 399 K G + 450 399 K H + 451 399 K I + 452 399 K M +453 399 K N + 454 399 K Q + 455 399 K R + 456 399 K S + 457 399 K T +458 399 K V + 459 399 K Y + 460 400 G E + 461 400 G K + 462 400 G S +463 401 Q A + 464 401 Q E + 465 401 Q S + 466 401 Q V + 467 406 G C +468 407 G A + 469 407 G K + 470 407 G L + 471 407 G R + 472 407 G S +473 407 G T + 474 408 C G + 475 408 C R + 476 408 C T + 477 408 C V +478 408 C W + 479 411 F A + 480 411 F L + 481 413 K A + 482 413 K P +483 413 K R + 484 413 K S + 485 415 N A + 486 416 F R + 487 416 F V +488 417 G Q + 489 417 G S + 490 418 Q A + 491 418 Q C + 492 418 Q E +493 418 Q G + 494 418 Q L + 495 418 Q T + 496 422 S M + 497 423 I V +498 423 I W + 499 424 E Q + 500 425 D A + 501 425 D E + 502 425 D G +503 425 D M + 504 425 D S + 505 425 D T + 506 426 Y L + 507 426 Y W +508 427 E A + 509 427 E L + 510 427 E M + 511 428 K R + 512 428 K R +513 428 K V + 514 429 S C + 515 429 S D + 516 429 S G + 517 429 S T +518 430 L M + 519 430 L V + 520 431 E A + 521 431 E F + 522 431 E G +523 431 E L + 524 431 E N + 525 432 A D + 526 432 A G + 527 432 A K +528 432 A L + 529 432 A R + 530 432 A S + 531 432 A V + 532 433 K E +533 433 K H + 534 433 K L + 535 433 K P + 536 433 K R + 537 433 K S +538 433 K V + 539 434 Q A + 540 434 Q C + 541 434 Q D + 542 434 Q F +543 434 Q G + 544 434 Q H + 545 434 Q K + 546 434 Q L + 547 434 Q R +548 437 A F + 549 437 A K + 550 437 A V + 551 438 A G + 552 438 A R +553 439 A R +

Megatable 2 MUT. Ref. ON OFF ON x Fold ONxOFF Fold NO. Pos. AA Sub. kcatRat. Rat. OFF vs. wt kcat vs. wt SEQ ID NO 1 210 0.17 0.03 0.0051 1.001.07 1.00 SEQ ID NO 2 34.2 0.74 0.21 0.15 30.0 5.25 4.90 330 331 L N40.4 0.75 0.43 0.32 63.0 12.99 12.14 551 438 A G 33.8 0.74 0.42 0.3160.3 10.41 9.73 331 331 L R 30.3 0.73 0.38 0.28 54.6 8.44 7.89 549 437 AK 35.7 0.76 0.36 0.27 52.9 9.63 9.00 552 438 A R 29.2 0.75 0.33 0.2548.5 7.23 6.76 406 385 L V 21.4 0.75 0.33 0.25 48.2 5.26 4.92 392 376 PW 23.1 0.68 0.34 0.23 46.0 5.42 5.07 489 417 G S 18.5 0.82 0.28 0.2345.2 4.26 3.98 69 161 G E 17.2 0.78 0.29 0.23 44.8 3.92 3.67 74 161 G Q27.7 0.77 0.30 0.23 44.8 6.33 5.91 553 439 A R 24.7 0.73 0.30 0.22 43.35.45 5.09 76 161 G S 24.5 0.76 0.29 0.22 43.2 5.41 5.06 133 182 L M 26.00.79 0.28 0.22 42.5 5.63 5.26 113 171 L F 16.6 0.75 0.28 0.21 41.8 3.543.31 268 215 R G 24.4 0.79 0.27 0.21 41.8 5.19 4.85 171 191 A S 12.40.75 0.28 0.21 40.8 2.59 2.42 59 158 P K 50.4 0.77 0.27 0.21 40.6 10.449.76 332 332 S A 41.5 0.75 0.28 0.21 40.5 8.58 8.02 79 161 G Y 21.6 0.780.26 0.20 40.0 4.40 4.11 405 385 L I 27.5 0.75 0.27 0.20 39.5 5.55 5.18329 331 L G 29.0 0.73 0.27 0.20 39.1 5.78 5.40 72 161 G N 23.5 0.78 0.250.20 38.6 4.63 4.33 488 417 G Q 20.6 0.74 0.27 0.20 38.4 4.04 3.77 70161 G L 14.0 0.77 0.25 0.19 37.8 2.71 2.53 60 159 A C 21.0 0.79 0.240.19 37.6 4.03 3.77 94 166 G P 11.4 0.77 0.25 0.19 37.2 2.17 2.03 93 166G A 23.1 0.77 0.24 0.19 36.4 4.29 4.01 328 331 L D 32.4 0.75 0.25 0.1836.2 5.98 5.59 98 169 F H 13.8 0.75 0.25 0.18 36.0 2.54 2.38 373 366 Q E20.1 0.75 0.24 0.18 34.9 3.58 3.35 400 382 T S 29.6 0.71 0.24 0.17 33.04.97 4.65 367 360 M L 26.5 0.77 0.22 0.17 32.6 4.41 4.12 418 390 R N30.3 0.75 0.22 0.17 32.4 5.00 4.67 144 189 D P 26.2 0.76 0.22 0.16 32.34.31 4.02 365 358 G E 15.5 0.69 0.23 0.16 31.5 2.49 2.33 362 356 E K38.8 0.75 0.21 0.16 31.2 6.18 5.78 226 206 P Q 35.4 0.74 0.21 0.16 30.85.57 5.20 167 191 A L 21.5 0.77 0.20 0.16 30.5 3.35 3.13 529 432 A R30.6 0.78 0.20 0.16 30.4 4.75 4.44 363 356 E R 39.1 0.75 0.21 0.15 30.05.97 5.58 335 340 R K 44.7 0.75 0.20 0.15 28.7 6.56 6.13 227 206 P S35.5 0.75 0.20 0.15 28.5 5.15 4.82 548 437 A F 12.7 0.76 0.19 0.14 28.11.82 1.70 263 214 S N 35.4 0.76 0.19 0.14 27.9 5.04 4.71 411 387 I L33.3 0.75 0.19 0.14 27.0 4.58 4.28 279 221 G V 9.8 0.75 0.18 0.13 26.11.30 1.21 527 432 A K 31.5 0.76 0.17 0.13 25.7 4.13 3.86 453 399 K N37.4 0.75 0.17 0.13 25.2 4.81 4.50 256 211 Y L 36.9 0.77 0.17 0.13 25.04.72 4.41 270 217 D Y 20.7 0.76 0.17 0.13 24.9 2.63 2.45 521 431 E F28.9 0.80 0.16 0.13 24.5 3.61 3.37 455 399 K R 34.8 0.74 0.17 0.12 23.64.18 3.91 438 396 K T 37.7 0.71 0.17 0.12 23.5 4.51 4.22 284 227 A G34.6 0.79 0.15 0.12 23.2 4.09 3.83 386 375 K L 36.1 0.71 0.16 0.12 22.84.20 3.92 357 352 N R 39.4 0.75 0.15 0.11 21.9 4.40 4.11 454 399 K Q36.1 0.72 0.15 0.11 21.5 3.96 3.70 435 396 K M 35.4 0.73 0.15 0.11 21.43.86 3.61 456 399 K S 35.8 0.70 0.15 0.11 21.3 3.90 3.64 547 434 Q R52.1 0.73 0.15 0.11 21.2 5.63 5.26 272 221 G A 42.2 0.62 0.17 0.10 20.34.37 4.09 266 214 S T 39.2 0.74 0.14 0.10 20.2 4.03 3.76 163 191 A G42.6 0.77 0.13 0.10 20.1 4.36 4.08 224 206 P K 21.9 0.74 0.14 0.10 19.92.23 2.08 342 342 A V 40.6 0.78 0.13 0.10 19.7 4.08 3.82 443 398 E D38.7 0.72 0.14 0.10 19.6 3.87 3.62 544 434 Q H 51.9 0.78 0.13 0.10 19.55.16 4.82 180 193 G Q 23.9 0.77 0.13 0.10 19.3 2.35 2.20 257 211 Y S18.9 0.79 0.12 0.10 19.1 1.83 1.71 158 190 G T 28.0 0.75 0.13 0.10 18.62.66 2.48 434 396 K L 40.5 0.57 0.17 0.09 18.6 3.85 3.60 530 432 A S34.6 0.72 0.13 0.09 18.6 3.28 3.06 21 56 A S 41.9 0.78 0.12 0.09 18.53.97 3.71 498 423 I W 36.7 0.48 0.19 0.09 18.0 3.37 3.15 402 383 F M45.9 0.70 0.13 0.09 17.5 4.11 3.84 225 206 P L 18.3 0.76 0.12 0.09 17.31.62 1.51 401 383 F L 47.2 0.66 0.13 0.08 16.3 3.92 3.67 339 342 A M52.3 0.73 0.11 0.08 16.0 4.28 4.00 25 125 R L 37.3 0.76 0.11 0.08 16.03.04 2.84 481 413 K A 39.0 0.59 0.13 0.08 15.5 3.09 2.88 265 214 S R25.4 0.75 0.10 0.08 14.9 1.94 1.81 546 434 Q L 55.5 0.71 0.11 0.08 14.84.20 3.93 7 53 L F 47.0 0.75 0.10 0.08 14.8 3.54 3.31 348 349 A Q 42.60.76 0.10 0.07 14.7 3.19 2.98 545 434 Q K 58.5 0.70 0.11 0.07 14.5 4.334.05 442 398 E A 42.8 0.72 0.10 0.07 14.4 3.14 2.93 337 342 A C 71.50.71 0.10 0.07 14.0 5.09 4.76 397 381 P N 55.8 0.74 0.10 0.07 13.7 3.913.66 387 375 K R 71.8 0.60 0.10 0.06 12.1 4.43 4.14 385 373 F V 49.20.76 0.08 0.06 12.0 3.01 2.81 347 349 A E 47.9 0.76 0.08 0.06 11.6 2.842.65 516 429 S G 50.2 0.74 0.08 0.06 11.6 2.97 2.78 517 429 S T 53.70.72 0.08 0.06 11.5 3.16 2.95 262 214 S M 22.6 0.74 0.07 0.06 10.9 1.251.17 492 418 Q E 83.8 0.69 0.05 0.04 7.1 3.03 2.83

Megatable 3 SEQ Variant ON OFF ON x ON x OFF x ID Name ratio ratio OFFkcat kcat 1 Mz wt 0.213 0.033 0.007 97.4 0.68 2 9070 0.744 0.116 0.08640.0 3.45 3 9070Q366E 0.760 0.273 0.208 20.1 4.18 4 P056028-A-01 0.6970.249 0.173 39.1 6.78 5 P056028-A-02 0.680 0.387 0.263 38.6 10.15 6P056028-F-05 0.700 0.395 0.276 27.4 7.57 7 P056028-G-01 0.742 0.3200.238 32.2 7.65 8 P056028-G-01R 0.719 0.280 0.201 70.8 14.24 9P056028-B-02 0.800 0.469 0.375 28.2 10.58 10 P056028-F-01 0.718 0.3040.218 31.3 6.82 11 P056028-D-08 0.681 0.361 0.246 27.5 6.77 12P056028-E-04 0.740 0.360 0.267 19.2 5.13 13 P056028-A-06 0.760 0.2810.214 27.0 5.77 14 P056028-F-02 0.730 0.430 0.314 28.2 8.84 15P056028-C-01 0.742 0.310 0.230 25.9 5.95 16 P056028-E-02 0.761 0.3260.248 23.6 5.86 17 P056028-C-07 0.714 0.382 0.273 21.2 5.80 18P056028-A-03 0.748 0.243 0.181 24.0 4.36 19 P056028-C-05 0.715 0.3750.268 21.7 5.80 20 P056028-A-08 0.669 0.324 0.217 26.2 5.68 21P056028-D-03 0.770 0.453 0.349 19.6 6.83 22 P056028-B-09 0.648 0.1870.121 34.5 4.19 23 P056028-A-10 0.707 0.367 0.260 16.8 4.35 24P056028-A-11 0.706 0.366 0.258 8.6 2.21 25 P056028-A-04 0.724 0.1330.096 11.1 1.06 26 P056028-A-05 0.707 0.280 0.198 17.7 3.50 27P056028-A-07 0.726 0.329 0.239 19.5 4.65 28 P056028-A-09 0.692 0.3390.235 13.9 3.26 29 P056028-B-01 0.745 0.309 0.230 18.6 4.28 30P056028-B-10 0.703 0.327 0.230 17.9 4.12 31 P056028-B-03 0.732 0.3530.259 17.9 4.63 32 P056028-B-04 0.718 0.273 0.196 16.5 3.24 33P056028-B-05 0.734 0.287 0.211 18.3 3.85 34 P056028-B-06 0.713 0.3530.252 20.0 5.03 35 P056028-B-07 0.788 0.389 0.307 9.2 2.83 36P056028-B-08 0.681 0.325 0.221 15.5 3.44 37 P056028-C-10 0.699 0.3560.249 14.6 3.63 38 P056028-C-11 0.731 0.293 0.214 12.3 2.64 39P056028-C-02 0.717 0.379 0.272 18.8 5.11 40 P056028-C-03 0.739 0.3560.263 13.7 3.62 41 P056028-C-04 0.727 0.322 0.234 22.7 5.32 42P056028-C-06 0.742 0.351 0.261 10.6 2.77 43 P056028-C-08 0.712 0.3810.271 13.5 3.65 44 P056028-C-09 0.706 0.314 0.222 17.0 3.76 45P056028-D-01 0.728 0.348 0.254 21.3 5.39 46 P056028-D-10 0.670 0.2530.170 18.1 3.07 47 P056028-D-11 0.719 0.261 0.188 17.1 3.21 48P056028-D-02 0.730 0.299 0.218 24.3 5.31 49 P056028-D-04 0.696 0.1970.137 12.4 1.71 50 P056028-D-05 0.730 0.508 0.371 12.6 4.66 51P056028-D-06 0.731 0.424 0.310 9.9 3.07 52 P056028-D-07 0.775 0.3700.286 9.1 2.60 53 P056028-D-09 0.652 0.371 0.242 13.0 3.16 54P056028-E-10 0.702 0.339 0.238 11.5 2.73 55 P056028-E-11 0.721 0.3040.219 16.9 3.70 56 P056028-E-03 0.735 0.412 0.303 16.9 5.10 57P056028-E-05 0.704 0.325 0.229 15.2 3.48 58 P056028-E-06 0.346 0.1860.064 28.2 1.76 59 P056028-E-07 0.585 0.262 0.153 20.6 3.08 60P056028-E-08 0.685 0.410 0.281 12.6 3.55 61 P056028-E-09 0.676 0.3080.208 14.9 3.10 62 P056028-F-10 0.726 0.291 0.211 13.7 2.89 63P056028-F-11 0.706 0.322 0.228 22.1 5.04 64 P056028-F-03 0.738 0.4910.363 13.0 4.73 65 P056028-F-04 0.660 0.245 0.161 16.7 2.70 66P056028-F-06 0.739 0.305 0.225 14.5 3.25 67 P056028-F-07 0.735 0.3220.236 21.4 5.04 68 P056028-F-08 0.705 0.377 0.266 12.1 3.23 69P056028-F-09 0.700 0.360 0.252 17.1 4.30 70 P056028-G-10 0.607 0.2590.157 29.3 4.61 71 P056028-G-02 0.761 0.304 0.231 23.0 5.30 72P056028-G-04 0.752 0.248 0.186 13.6 2.54 73 P056028-G-05 0.739 0.3610.267 16.7 4.47 74 P056028-G-06 0.725 0.382 0.277 12.0 3.30 75P056028-G-07 0.702 0.304 0.213 15.3 3.23 76 P056028-G-08 0.737 0.3790.279 11.8 3.29 77 P056028-G-09 0.716 0.385 0.275 15.8 4.37

That which is claimed:
 1. A plant cell comprising a nucleic acidconstruct comprising a polynucleotide sequence encoding a polypeptidehaving 4-hydroxyphenylpyruvate dioxygenase (HPPD) activity andcomprising the amino acid sequence of SEQ ID NO: 3, wherein the aminoacid at 158 is Pro and Lys, the amino acid at position 182 is Leu orMet, the amino acid at position 191 is Ala or Gly, the amino acid atposition 206 is Pro, Gln, or Ser, the amino acid at position 211 is Tyror Leu, the amino acid at position 214 is Ser or Asn, the amino acid atposition 340 is Arg or Lys, the amino acid at position 356 is Glu, Lysor Arg, the amino acid at position 385 id Leu, Ile or Val, the aminoacid at position 387 is Ile or Leu, the amino acid at position 417 isGly, Gln or Ser, the amino acid at position 432 is Ala, Arg or Lys, andthe amino acid at position 434 is Gln, His, or Arg; wherein thepolypeptide has improved insensitivity to an HPPD inhibitor compared tothe polypeptide of SEQ ID NO:
 1. 2. The plant cell of claim 1, whereinthe nucleic acid construct further comprises a promoter operably linkedto the polynucleotide sequence.
 3. The plant cell of claim 1, whereinthe plant cell has an improved insensitivity to an HPPD inhibitorcompared to a wild type plant cell of the same species, strain orcultivar.
 4. The plant cell of claim 1, wherein the plant cell furthercomprises at least one additional polypeptide imparting tolerance to anadditional herbicide.
 5. The plant cell of claim 4, wherein the at leastone polypeptide imparting tolerance to an additional herbicidecomprises: (a) a sulfonylurea-tolerant acetolactate synthase; (b) animidazolinone-tolerant acetolactate synthase; (c) a glyphosate-tolerant5-enolpyruvylshikimate-3-phosphate synthase; (d) a glyphosate-tolerantglyphosate oxido-reductase; (e) a glyphosate-N-acetyltransferase; (f) aphosphinothricin acetyl transferase; (g) a protoporphyrinogen oxidase,(h) an AAD1 or AAD12; or (i) a P450 polypeptide NSF1; or (j) an acetylcoenzyme A carboxylase (ACCase).
 6. The plant cell of claim 4, whereinthe at least one polypeptide imparting tolerance to an additionalherbicide comprises an HRA high resistance allele of acetolactatesynthase and/or a glyphosate-N-acetyltransferase polypeptide.
 7. Theplant cell of claim 4, wherein the plant cell further comprises at leastone additional polypeptide imparting tolerance to an HPPD herbicide. 8.A plant comprising the plant cell of any of claim
 1. 9. A transgenicseed produced by the plant of claim 8.